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Cited by 426Metalloenzymes and iron-sulfur proteinsWastewater Treatment and Nitrogen RemovalEnzyme Structure and Function

Nitrate and periplasmic nitrate reductases

Open access
Sparacino-Watkins, Courtney, Stolz, John F., Basu, Partha·2014·Chem. Soc. Rev.
DOI 10.1039/c3cs60249dPMC PMC4080430
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Abstract

The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.

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Written from the paper’s full text.

TL;DR

This review summarizes nitrate in the nitrogen cycle and human health and focuses on periplasmic nitrate reductase (Nap), its structure, kinetics, auxiliary proteins, operon organization, and phylogeny. It emphasizes that Nap is functionally diverse despite conserved catalytic features, with genetic and regulatory variability across Proteobacteria.

Key findings

  • Nitrate is central to the global nitrogen cycle and human health: the USA EPA maximum contaminant level for nitrate in drinking water is 10 mg L−1, the WHO level is 50 mg L−1, and nitrite has an MCL of 1 mg L−1; nitrate in vegetables ranges from 13 mg kg−1 in asparagus to 2500 mg kg−1 in spinach. Nitrate reduction to nitrite is linked to methemoglobinemia in infants and to NO-related cardiovascular and host-defense effects.
  • Nap catalyzes nitrate reduction to nitrite at a molybdenum center and generally has high nitrate affinity, with micromolar Km values (less than 300 µM) and a Vmax of ~2 µmol min−1 mg−1. The Mo active site is buried ~15 Å inside the protein, NapA sizes range from 70 kDa to 105 kDa, and revised structures of D. desulfuricans and C. necator NapA identify a sixth Mo ligand as sulfide rather than oxo.
  • Nap is functionally diverse, implicated in denitrification, dissimilatory nitrate reduction to ammonia, redox poise, nitrate scavenging, nitrate respiration, and pathogenicity. Auxiliary proteins vary: NapB is essential in some organisms, NapD is essential for nitrate reduction in R. sphaeroides, E. coli, and W. succinogenes, and NapF aids [4Fe–4S] insertion.
  • The nap operon is variable, with at least 11 nap genes and at least 4 distinct operons (EDABC, DAGHBC, CMADGH, and AGHBFLD). A neighbor-joining tree of 288 NapA sequences plus three assimilatory nitrate reductases and one formate dehydrogenase outgroup resolved four major subclades that correlate with operon organization; monomeric D. desulfuricans NapA is most similar to assimilatory nitrate reductase.

Methods

  • Design: narrative review with two major sections—first, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations, and structural/redox chemistry; second, periplasmic nitrate reductase, including NapA kinetics, auxiliary Nap proteins, operon structure, and phylogenetic relationships.
  • Data/sample: synthesis of published biochemical, structural, spectroscopic, genetic, and physiological literature; no primary experimental data are reported by the authors.
  • Main analysis: literature synthesis plus a neighbor-joining phylogenetic tree from multiple sequence alignments of 288 NapA sequences with three assimilatory nitrate reductases and one formate dehydrogenase outgroup; operon gene orders are also tabulated across 26 strains representing 19 Shewanella species.

Limitations

  • Stated: crystallography alone cannot unambiguously define coordination spheres, especially for lower-resolution structures and because of possible radiation damage; a complete picture requires spectroscopic information calibrated with well-defined discrete inorganic compounds. The mechanistic details of the Mo(vi) center and catalytic cycle remain to be fully appreciated, and no experimental evidence is available to confirm whether NapS is translated or what its function may be.
  • Stated: many organisms described in the review have been renamed, some several times, posing a challenge to track what has been studied on which organism.
  • Evident: as a narrative review, no systematic literature search or inclusion criteria are described, so conclusions rely on cited primary studies and may be constrained by the available sequence, structural, and mechanistic data at the time of writing.

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Integrity signals

Registry

Crossref · 10.1039/c3cs60249d

Cites

340 of 340 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 243 cited sources checked · 0 supported · 0 flagged

  • Findingcitation

    Biogenic magnetite formation by Magnetospirillum gryphiswaldense requires periplasmic nitrate reductase (Nap).

    “In a recent study, Li et al. have shown that biogenic magnetite formation by Magnetospirillum gryphiswaldense requires periplasmic nitrate reductase (Nap).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [87] Li Y Katzmann E Borg S Schueler D J. Bacteriol 2012 194 4847 4856 22730130 PMC3430331 source

      Not checked in the free run.

  • Findingcitation

    Sulfurospirillum barnesii couples lactate oxidation to dissimilatory nitrate reduction to ammonia.

    “For example, Sulfurospirillum barnesii has been shown to couple lactate oxidation to dissimilatory nitrate reduction to ammonia.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [95] Oremland RS Blum JS Culbertson CW Visscher PT Miller LG Dowdle P Strohmaier FE Appl. Environ. Microbiol 1994 60 3011 3019 16349362 PMC201757 source

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  • Findingcitation

    When nitrate reduction is coupled to formate oxidation, a proton gradient is generated across the cell membrane.

    “In reality, when nitrate reduction is coupled to formate oxidation, a proton gradient is indeed generated across the cell membrane.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [96] Jepson BJN Mohan S Clarke TA Gates AJ Cole JA Butler CS Butt JN Hemmings AM Richardson DJ J. Biol. Chem 2007 282 6425 6437 17130127 source

      Not checked in the free run.

  • Findingown data

    The angles from the DMSOR family cluster at a different position than those from the SO family and members of the XO family.

    “When looked at closely, the structures from NR (excluding the ring open cofactor) and structures of enzymes belonging to the XO and SO families, it appears that the angles from the DMSOR family cluster at a different position than those from SO, and members of the XO family (Fig. 5).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Fig. 5

      Not checked in the free run.

    • Rests on an assumption: The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.
  • Findingown data

    For most structures, the <OCCS and <OCCC angles linearly correlate, with exceptions in a few DMSOR and formate dehydrogenase (FDH) structures.

    “For most structures, the angles linearly correlate with the exception of a few DMSOR and formate dehydrogenase (FDH) structures that may reflect the quality of the structure rather than an intrinsic property of the cofactor.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: For most crystallographically determined structures, the <OCCS and <OCCC torsion angles reflect the intrinsic geometry of the pterin cofactor rather than artifacts of structure quality.
  • May combine two claims. 75
  • Classified as probably not a substantial claim. 56
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingcitation

    Nap fractionates with an O-to-N ratio of ~0.6 and has a limited effect on the overall pool of nitrate reduction in the environment.

    “The periplasmic nitrate reductase (Nap) fractionates with an O-to-N ratio of ~0.6, and is considered to have a limited effect on the overall pool of nitrate reduction in the environment.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [86] Karsh KL Granger J Kritee K Sigman DM Environ. Sci. Technol 2012 46 5727 5735 22534036

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Nap deletion mutants of M. gryphiswaldense exhibit attenuated growth and production of magnetite crystals.

    “Nap deletion mutants of M. gryphiswaldense exhibit attenuated growth and production of magnetite crystals.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [87] Li Y Katzmann E Borg S Schueler D J. Bacteriol 2012 194 4847 4856 22730130 PMC3430331

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Several functionally diverse Nap enzymes have been isolated from a variety of prokaryotes.

    “Since the first report of Nap several functionally diverse Nap enzymes have been isolated from a variety of prokaryotes (see Section 3.6.1, Table 7).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    Epsilonproteobacteria only contain Nap yet are capable of anaerobic nitrate respiration.

    “The Epsilonproteobacteria only contain Nap yet are capable of anaerobic nitrate respiration.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [93] Kern M Simon J Biochim. Biophys. Acta, Bioenerg 2009 1787 646 656 19171117

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Unaccompanied Nap and pNar are not capable of producing a proton motive force across the inner membrane; however nitrate reduction coupled to formate oxidation generates a proton gradient across the cell membrane.

    “Unaccompanied Nap and pNar are not capable of producing a proton motive force across the inner membrane; however nitrate reduction when coupled to formate oxidation does indeed generate a proton gradient across the cell membrane (see below).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [93] Kern M Simon J Biochim. Biophys. Acta, Bioenerg 2009 1787 646 656 19171117

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    • cites [96] Jepson BJN Mohan S Clarke TA Gates AJ Cole JA Butler CS Butt JN Hemmings AM Richardson DJ J. Biol. Chem 2007 282 6425 6437 17130127

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Nap proteins have been associated with pathogenicity in Helicobacter and Campylobacter, where Nap genes are up-regulated in response to oxidative stress.

    “Nap proteins have also been associated with pathogenicity in Helicobacter and Campylobacter, where Nap genes are up-regulated in response to oxidative stress.”
    Quote in the paperNot a substantial claim0 of 6 sources checked
    • cites [73] Weingarten RA Grimes JL Olson JW Appl. Environ. Microbiol 2008 74 1367 1375 18192421 PMC2258625

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    • cites [106] Cooksley C Jenks PJ Green A Cockayne A Logan RPH Hardie KR J. Med. Microbiol 2003 52 461 469 12748264

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    • cites [107] Vegge CS Brondsted L Li Y-P Bang DD Ingmer H Appl. Environ. Microbiol 2009 75 5308 5314 19542337 PMC2725471

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    • cites [108] Spiro S FEMS Microbiol. Rev 2007 31 193 211 17313521

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    • cites [109] Taveirne ME Sikes ML Olson JW Mol. Microbiol 2009 74 758 771 19919002

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    • cites [110] Pittman MS Kelly DJ Biochem. Soc. Trans 2005 33 190 192 15667303

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  • May combine two claims.

    Findingcitation

    The Mo-center of D. desulfuricans NapA was initially proposed to contain a terminal oxo-group, but later redetermination revealed a terminal sulfido group.

    “Initially the Mo-center was proposed to contain a terminal oxo-group. Later redetermination of the structure revealed a terminal sulfido group instead of an oxo-group.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [120] Najmudin S Gonzalez PJ Trincao J Coelho C Mukhopadhyay A Cerqueira NMFSA Romao CC Moura I Moura JJG Brondino CD Romao MJ JBIC, J. Biol. Inorg. Chem 2008 13 737 753 18327621

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  • May combine two claims.

    Findingnone given

    In structures where the pyran ring is open, the observed <OCCS angle values are lower and <OCCC angle values are higher, even though they fall on the same line.

    “In structures where the pyran ring is open, the observed values of <OCCS angle are lower while <OCCC angles are of higher value, even though they fall on the same line.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    In Nap and Nar, the presence of two pterin cofactors has been unequivocally established; no such information for Nas is yet available.

    “In the case of Nap and Nar the presence of two pterin cofactors has been unequivocally established, however, no such information for Nas is yet available.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    In all NapA and eukNR structures determined to date, the pyran ring of the pyranopterin cofactor is in the closed form; however, the distal pyranopterin ring is open in E. coli Nar.

    “In all NapA and eukNR structures determined to date, the pyran ring of the pyranopterin cofactor is in the closed form; however, the distal pyranopterin ring is open in E. coli Nar (Fig. 4).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    In crystallographically characterized pterin-containing molybdenum enzymes, the Mo-center is found to be nearly 15 Å inside the protein, and Nap is no exception.

    “In crystallographically characterized pterin-containing molybdenum enzymes, the Mo-center is found to be nearly 15 Å inside the protein and Nap is no exception.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Most representatives of the SO family analyzed were from mammalian sources, while the NR representatives were from microbial sources.

    “Most representatives of the SO family analyzed here were from mammalian sources, while the NR representatives were from microbial sources.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In plants and fungi, eukNR functions in nitrate assimilation, while the three prokaryote nitrate reductases can function in both assimilatory and dissimilatory nitrate reduction.

    “In plants and fungi, eukNR functions in nitrate assimilation, while the three prokaryote nitrate reductases can function in both assimilatory and dissimilatory nitrate reduction: assimilatory nitrate reductase (Nas) or dissimilatory nitrate reductases i.e., Nar and Nap.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [76] Stolz JF Basu P ChemBioChem 2002 3 198 206 11921398

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Nitrate reductases are divided into four major groups: eukNR, Nas, Nap, and Nar.

    “All nitrate reductases are molybdenum dependent enzymes, and have been divided into four major groups: eukNR, Nas, Nap, and Nar.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [76] Stolz JF Basu P ChemBioChem 2002 3 198 206 11921398

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  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Nap proteins from different Proteobacteria are phylogenetically distinct despite similarities in their catalytic and spectroscopic properties.

    “Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Animals do not encode a classical nitrate reductase, although bovine xanthine oxidase can reduce nitrate into nitrite.

    “Eukaryotic nitrate reductase (eukNR) has been isolated from plants and fungi; animals do not encode a classical nitrate reductase, although bovine xanthine oxidase (XO) can reduce nitrate into nitrite.”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [77] Li H Samouilov A Liu X Zweier JL Biochemistry 2003 42 1150 1159 12549937 source

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    • cites [78] Millar TM Stevens CR Benjamin N Eisenthal R Harrison R Blake DR FEBS Lett 1998 427 225 228 9607316 source

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    • cites [79] Li H Samouilov A Liu X Zweier JL J. Biol. Chem 2001 276 24482 24489 11312267 source

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    • cites [80] Jansson EA Huang L Malkey R Govoni M Nihlen C Olsson A Stensdotter M Petersson J Holm L Weitzberg E Lundberg JO Nat. Chem. Biol 2008 4 411 417 18516050 source

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  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    The physiological role of NapA is diverse.

    “Despite catalytic consistencies and confinement in the periplasmic space, the physiological role of NapA is diverse.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    All nitrate reductases are molybdopterin enzymes with molybdenum ligated by one or two pyranopterin prosthetic groups at the catalytic site.

    “All nitrate reductases are molybdopterin enzymes, where molybdenum is explicitly ligated by one or two pyranopterin prosthetic groups at the enzyme’s catalytic heart.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    Assimilatory NRs (eukNR and Nas) are soluble cytoplasmic proteins, while dissimilatory NRs (Nap and Nar) are membrane associated.

    “The assimilatory NRs (both eukNR and Nas) are soluble, cytoplasmic proteins, while the dissimilatory NRs (i.e., Nap and Nar) are membrane associated.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The periplasmic nitrate reductase (Nap) was first purified from Paracoccus denitrificans in 1993.

    “The periplasmic nitrate reductase (Nap) was first purified from Paracoccus denitrificans in 1993.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [94] Sears HJ Ferguson SJ Richardson DJ Spiro S FEMS Microbiol. Lett 1993 113 107

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Nap was initially differentiated from Nar by its cellular location, insensitivity to azide, and inability to reduce chlorate.

    “Initially, it was differentiated from the well-known respiratory nitrate reductases (Nar) not just by its cellular location but also by its insensitivity to azide and its inability to reduce chlorate.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [94] Sears HJ Ferguson SJ Richardson DJ Spiro S FEMS Microbiol. Lett 1993 113 107

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The pyranopterin cofactor should be taken as a 'dihydropterin'.

    “Thus, the pyranopterin cofactor should be taken as a ‘dihydropterin’.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [111] Basu P Burgmayer SJN Coord. Chem. Rev 2011 255 1016 1038 21607119 PMC3098623

      Not checked in the free run.

    • cites [112] Fischer B Enemark JH Basu P J. Inorg. Biochem 1998 72 13 21 9861725

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    The exceptions among DMSOR and FDH structures may reflect the quality of the structure rather than an intrinsic property of the cofactor.

    “For most structures, the angles linearly correlate with the exception of a few DMSOR and formate dehydrogenase (FDH) structures that may reflect the quality of the structure rather than an intrinsic property of the cofactor.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: For most crystallographically determined structures, the <OCCS and <OCCC torsion angles reflect the intrinsic geometry of the pterin cofactor rather than artifacts of structure quality.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The catalytic subunit of periplasmic nitrate reductase from Desulfovibrio desulfuricans, NapA, was the first nitrate reductase to be structurally characterized.

    “The catalytic subunit of periplasmic nitrate reductase from Desulfovibrio desulfuricans, NapA, was the first nitrate reductase to be structurally characterized.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [119] Dias J Than M Humm A Bourenkov GP Bartunik HD Bursakov S Calvete J Caldeira J Carneiro C Moura JJ Moura I Romao MJ Structure 1999 7 65 79 10368307

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Mycobacterium and Pseudomonas utilize nitrate reductases during host (lung) infection, suggesting nitrate reduction is important to the physiology of pathogens.

    “Mycobacterium and Pseudomonas also utilize nitrate reductases during host (lung) infection, suggesting nitrate reduction is important to the physiology of pathogens.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [70] Khan A Sarkar D Microbiology 2012 158 301 307 22174380

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    • cites [71] Weber I Fritz C Ruttkowski S Kreft A Bange F-C Mol. Microbiol 2000 35 1017 10712684

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    • cites [72] Palmer KL Brown SA Whiteley M J. Bacteriol 2007 189 4449 4455 17400735 PMC1913347

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  • May combine two claims.

    Interpretationreasoning

    The different geometric features are related to different redox states of the pterin, suggesting that redox states of the pterin are fundamentally different in NR and SO.

    “The different geometric features are related to different redox states of the pterin, which suggests that redox states of the pterin are fundamentally different in NR and SO.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.

  • May combine two claims.

    Interpretationnone given

    The pyran ring can protect a reduced state of the pterin cofactor and influence the orientation of the cofactor in the protein milieu, possibly modulating electron transfer.

    “The pyran ring can not only protect a reduced state of the pterin cofactor but also influence the orientation of the cofactor in the protein milieu, possibly modulating electron transfer.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.

  • May combine two claims.

    Interpretationcitation

    The redox state of the pterin allows tuning of the redox state of the metal center and vectorial electron transfer in NapA, which has two pyranopterin cofactors coordinating the Mo-center.

    “Implication of this finding is that the redox state of the pterin allows tuning of the redox state of the metal center and vectorial electron transfer in the case of NapA, which has two pyranopterin cofactors coordinating the Mo-center.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Model studies have shown that the topological feature protects the Mo-centers from dimerization and changes the electronic structure of the center via modulation of metal-sulfur covalency.

    “Model studies have shown that not only does this topological feature protect the Mo-centers from dimerization,140,141 but also changes the electronic structure of the center via modulation of metal–sulfur covalency.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [140] Mondal S Basu P Inorg. Chem 2001 40 192 193 11170521

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    • cites [141] Sengar RS Basu P Inorg. Chim. Acta 2007 360 2092 2099 PMC2040077 18425212

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  • May combine two claims.

    Premisereasoning

    In the Mo(iv) state the dxy orbital is fully occupied and is empty in the Mo(vi) state.

    “In the Mo(iv) state the dxy orbital is fully occupied and is empty in the Mo(vi) state.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The energy of the dxy orbital can be altered through small perturbations in the geometry around the molybdenum center, and solvation of the center preferentially stabilizes the higher charges.

    “The energy of this orbital can be altered through small perturbations in the geometry around the molybdenum center (e.g., changing the torsion angle of the coordinated amino acid, changing the fold angle of dithiolene ligand) and solvation of the center preferentially stabilizes the higher charges.150–153”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [150] Nemykin VN Basu P Inorg. Chem 2003 42 4046 4056 12817960

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    • cites [151] Kail B Nemykin VN Davie SR Carrano CJ Hammes B Basu P Inorg. Chem 2002 41 1281 1291 11874366

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    • cites [152] Davie SR Rubie ND Hammes BS Carrano CJ Kirk ML Basu P Inorg. Chem 2001 40 2632 2633 11375669

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    • cites [153] Inscore FE Knottenbelt SZ Rubie ND Joshi HK Kirk ML Enemark JH Inorg. Chem 2006 45 967 976 16441102

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  • May combine two claims.

    Premisenone given

    The terminal oxo-group in oxo-molybdenum complexes dominates the ligand field, making the dxy orbital energetically isolated and the lowest in energy among the 4d orbitals.

    “The terminal oxo-group in oxo-molybdenum complexes dominate the ligand field making the dxy orbital energetically isolated and the lowest in energy among the 4d orbitals.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In desoxo-Mo complexes, the dominating effect of the terminal oxo group is absent, and the dithiolene ligand effectively dictates the Mo ligand field, resulting in an isolated dxy orbital in the ground state.

    “In the desoxo-Mo complexes, the dominating effect of the terminal oxo group is absent,144–148 and the dithiolene ligand effectively dictates the Mo ligand field, again resulting in an isolated dxy orbital in the ground state.149”
    Quote in the paperSubstantial claim0 of 6 sources checked
    • cites [144] Lim BS Holm RH J. Am. Chem. Soc 2001 123 1920 1930 11456813

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    • cites [145] Lorber C Donahue JP Goddard CA Nordlander E Holm RH J. Am. Chem. Soc 1998 120 8102 8112

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    • cites [146] Lim BS Sung K-M Holm RH J. Am. Chem. Soc 2000 122 7410 7411

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    • cites [147] Majumdar A Pal K Nagarajan K Sarkar S Inorg. Chem 2007 46 6136 6147 17580939

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    • cites [148] Majumdar A Pal K Sarkar S Dalton Trans 2009 1927 1938 19259562

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    • cites [149] McNaughton RL Lim BS Knottenbelt SZ Holm RH Kirk ML J. Am. Chem. Soc 2008 130 4628 4636 18341333

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  • May combine two claims.

    Premisecitation

    Based on crystallographic analysis, Rothery et al. suggested the redox state of the pterin in sulfite oxidase is dihydro, in xanthine oxidase is tetrahydro, and the two pterins in DMSO reductases are in tetrahydro and dihydro forms.

    “Based on a detailed analysis of the conformation of the pterin cofactor as determined from crystallography, Rothery et al.130 suggested the redox state of the pterin in different enzymes are as follows: sulfite oxidase in dihydro, xanthine oxidase in tetrahydro, the two pterins in DMSO reductases are in tetrahydro and dihydro forms.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Rothery et al.130 Rothery RA Stein B Solomonson M Kirk ML Weiner JH Proc. Natl. Acad. Sci. U. S. A 2012 109 14773 14778 22927383 PMC3443133

      Not checked in the free run.

    • Rests on an assumption: The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    The net transfer of the oxygen atom, a two-electron transfer process, can occur either via a hydroxylation or by a formal atom transfer process.

    “The net transfer of the oxygen atom, a two-electron transfer process, can occur either via a hydroxylation or by a formal atom transfer processes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The reduction of nitrate to nitrite occurs at the molybdenum site of NRs, requires two electrons, and is coupled with the transfer of two protons.

    “The reduction of nitrate to nitrite occurs at the molybdenum site of NRs, and it requires two electrons and is coupled with the transfer of two protons.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Such reactions may proceed via multiple transition states involving an associative transition state and formation of a product bound intermediate.

    “Such reactions may proceed via multiple transition states involving an associative transition state and formation of a product bound intermediate.164–172”
    Quote in the paperNot a substantial claim0 of 9 sources checked
    • cites [164] Basu P Kail BW Young CG Inorg. Chem 2010 49 4895 4900 20433155 PMC2897133

      Not checked in the free run.

    • cites [165] Basu P Nemykin VN Sengar RS Inorg. Chem 2009 48 6303 6313 19485389

      Not checked in the free run.

    • cites [166] Kail BW Perez LM Zaric SD Millar AJ Young CG Hall MB Basu P Chem.-Eur. J 2006 12 7501 7509 16865754

      Not checked in the free run.

    • cites [167] Millar AJ Doonan CJ Smith PD Nemykin VN Basu P Young CG Chem.-Eur. J 2005 11 3255 3267 15786505

      Not checked in the free run.

    • cites [168] Nemykin VN Basu P Inorg. Chem 2005 44 7494 7502 16212375

      Not checked in the free run.

    • cites [169] Nemykin VN Laskin J Basu P J. Am. Chem. Soc 2004 126 8604 8605 15250684

      Not checked in the free run.

    • cites [170] Sengar RS Nemykin VN Basu P J. Inorg. Biochem 2008 102 748 756 18187198 PMC2396449

      Not checked in the free run.

    • cites [171] Smith PD Millar AJ Young CG Ghosh A Basu P J. Am. Chem. Soc 2000 122 9298 9299

      Not checked in the free run.

    • cites [172] Basu P Kail BW Adams AK Nemykin VN Dalton Trans 2013 42 3071 3081 23212540 PMC3566299

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Because only one oxygen atom is transferred to or from the substrate, these enzymes can be viewed as a monooxygenase.

    “Because only one oxygen atom is transferred to or from the substrate, these enzymes can be viewed as a monooxygenase.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    In oxidases such as SO, a water molecule serves as a source of the oxygen atom.

    “In oxidases, such as SO a water molecule serves as a source of the oxygen atom.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The oxygen atom in nitrate to nitrite transformation forms a water molecule coupling with the proton.

    “The oxygen atom in nitrate to nitrite transformation forms a water molecule coupling with the proton mentioned above.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Direct atom transfer processes have been demonstrated with model complexes.

    “Direct atom transfer processes have been demonstrated with model complexes, and have been summarized elsewhere.126,139,158–163”
    Quote in the paperNot a substantial claim0 of 8 sources checked
    • cites [126] Sugimoto H Tsukube H Chem. Soc. Rev 2008 37 2609 2619 19020675

      Not checked in the free run.

    • cites [139] Holm RH Coord. Chem. Rev 1990 100 183 221

      Not checked in the free run.

    • cites [158] Holm RH Solomon EI Majumdar A Tenderholt A Coord. Chem. Rev 2011 255 993 1015

      Not checked in the free run.

    • cites [159] Young CG Biomimetic Oxidations Catalyzed by Transition Metal Complexes 2000 Imperial College Press 415 459

      Not checked in the free run.

    • cites [160] McMaster J Tunney JM Garner CD Prog. Inorg. Chem 2003 52 539 583

      Not checked in the free run.

    • cites [161] Enemark JH Cooney JJA Wang J-J Holm RH Chem. Rev 2004 104 1175 1200 14871153

      Not checked in the free run.

    • cites [162] Enemark JH Young CG Adv. Inorg. Chem 1994 40 1 88

      Not checked in the free run.

    • cites [163] Holm RH Chem. Rev 1987 87 1401 1449

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The redox potential of the nitrate-nitrite couple is highly positive (+433 mV), justifying the ease of its reduction.

    “Of the substrates, the redox potential of the nitrate–nitrite couple is highly positive (+433 mV) justifying the ease of its reduction.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The DMSO reductase and SO family of enzymes function via atom transfer process, while XO members function via hydroxylation.

    “It is believed that the DMSO reductase and SO family of enzymes function via atom transfer process,154 while XO members function via hydroxylation.155–157”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [154] Schultz BE Hille R Holm RH J. Am. Chem. Soc 1995 117 827 828

      Not checked in the free run.

    • cites [155] Choi E-Y Stockert AL Leimkuhler S Hille R J. Inorg. Biochem 2004 98 841 848 15134930

      Not checked in the free run.

    • cites [156] Hille R Biochemistry 1991 30 8522 8529 1888720

      Not checked in the free run.

    • cites [157] Kim JH Ryan MG Knaut H Hille R J. Biol. Chem 1996 271 6771 6780 8636099

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In most cases, including nitrate reductase, the intermediate +5 oxidation state of molybdenum has been characterized by EPR spectroscopy.

    “In most cases, including nitrate reductase, the intermediate +5 oxidation state of molybdenum has been characterized by electron paramagnetic (EPR) spectroscopy.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    While the redox potentials of the substrate half reactions can vary significantly, the redox potential of the Mo-centers do not change as much.

    “It is interesting to note that while the redox potentials of the substrate half reactions (Table 3) can vary significantly, the redox potential of the Mo-centers do not change as much.113”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [113] Hille R Chem. Rev 1996 96 2757 2816 11848841

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A pterin unit in dihydro state can carry out two electron chemistry, and a pterin based radical has been detected in AO.

    “A pterin unit in dihydro state can carry out two electron chemistry,112,184 and pterin based radical has been detected in AO.185”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [112] Fischer B Enemark JH Basu P J. Inorg. Biochem 1998 72 13 21 9861725

      Not checked in the free run.

    • cites [184] Burgmayer SNJ Pearsall DL Blaney SM Moore EM Sauk-Schubert C JBIC, J. Biol. Inorg. Chem 2004 9 59 66 14628171

      Not checked in the free run.

    • cites [185] Luykx DMAM Duine JA de Vries S Biochemistry 1998 37 11366 11375 9698384

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    During the two-electron substrate transformation, the metal center changes its redox state by two units, and the catalytically competent center is regenerated in two one-electron steps.

    “During the two-electron substrate transformation, the metal center changes its redox state by two units, and the catalytically competent center is regenerated in two one-electron steps.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    The Mo center shuttles between +4 and +6 oxidation states, thus can carry out two-electron chemistry.

    “The Mocenter shuttles between +4 and +6 oxidation states, thus can carry out two-electron chemistry.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    During the electron regeneration process, the Mo center is reduced via physiological partners such as quinones or hemes.

    “During the electron regeneration process, the Mo center is reduced via physiological partners such as quinones, or hemes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The dithiolene ligand can carry out two-electron chemistry from fully reduced dithiolene to fully oxidized dithione, and these redox states have been experimentally demonstrated.

    “The dithiolene ligand can also carry out two-electron chemistry from fully reduced dithiolene to fully oxidized dithione, and these redox states have been experimentally demonstrated.178–183”
    Quote in the paperSubstantial claim0 of 6 sources checked
    • cites [178] Perera E Basu P Dalton Trans 2009 5023 5028 19662295 PMC2894468

      Not checked in the free run.

    • cites [179] Nemykin VN Olsen JG Perera E Basu P Inorg. Chem 2006 45 3557 3568 16634586

      Not checked in the free run.

    • cites [180] Sproules S Banerjee P Weyhermuller T Yan Y Donahue JP Wieghardt K Inorg. Chem 2011 50 7106 7122 21699192

      Not checked in the free run.

    • cites [181] Sproules S Wieghardt K Coord. Chem. Rev 2011 255 837 860

      Not checked in the free run.

    • cites [182] Mtei RP Perera E Mogesa B Stein B Basu P Kirk ML Eur. J. Inorg. Chem 2011 5467 5470 23956683 PMC3742805

      Not checked in the free run.

    • cites [183] Matz KG Mtei RP Rothstein R Kirk ML Burgmayer SJN Inorg. Chem 2011 50 9804 9815 21894968 PMC3268461

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Tyrosine-58 is conserved in all heterodimeric NapA but absent in monomeric NapA such as D. desulfuricans.

    “conserved in all heterodimeric NapA, but absent in monomeric NapA such as D. desulfuricans.186”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [186] Arnoux P Sabaty M Alric J Frangioni B Guigliarelli B Adriano J-M Pignol D Nat. Struct. Biol 2003 10 928 934 14528294 source

      Not checked in the free run.

  • May combine two claims.

    Premiseown data

    NapA contains two redox active centers: a molybdenum active site and an iron sulfur cluster.

    “NapA contains two redox active centers: a molybdenum active site and an iron sulfur cluster (Fig. 7).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Fig. 7

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Molybdenum centers coordinated by two pyranopterins can provide up to ten-electron chemistry, making it one of the most electron rich redox active centers in biology.

    “Thus, in principle, molybdenum centers coordinated by two pyranopterins can provide up to ten-electron chemistry, making it one of the most electron rich redox active centers in biology.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The crystal structures of NapA from Cupriavidus necator (PDB ID: 3ML1), E. coli (PDB ID: 2NYA), R. sphaeroides (PDB ID: 1OGY), and D. desulfuricans (PDB ID: 2NAP) have been reported.

    “The crystal structures of NapA from several species have been reported: Cupriavidus necator (PDB ID: 3ML1),121 E. coli (PDB ID: 2NYA),96 R. sphaeroides (PDB ID: 1OGY),186 and D. desulfuricans (PDB ID: 2NAP).119”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [121] Coelho C Gonzalez PJ Moura JG Moura I Trincao J Romao MJ J. Mol. Biol 2011 408 932 948 21419779 source

      Not checked in the free run.

    • cites [96] Jepson BJN Mohan S Clarke TA Gates AJ Cole JA Butler CS Butt JN Hemmings AM Richardson DJ J. Biol. Chem 2007 282 6425 6437 17130127 source

      Not checked in the free run.

    • cites [186] Arnoux P Sabaty M Alric J Frangioni B Guigliarelli B Adriano J-M Pignol D Nat. Struct. Biol 2003 10 928 934 14528294 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    These descriptions were consistent with the spectroscopically characterized Mo(v) state where it is generally accepted that a water or hydroxyl group coordinates to the Mo-center.

    “These descriptions were consistent with the spectroscopically characterized Mo(v) state where it is generally accepted that a water or hydroxyl group coordinates to the Mo-center.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    In the initial structure of NapA from D. desulfuricans, the sixth ligand was assigned as a terminal oxo, and in subsequent structures of NapAB from E. coli and R. sphaeroides the sixth ligand to the oxidized molybdenum center was viewed as a coordinated water or hydroxo ligand.

    “In the initial structure of NapA from D. desulfuricans, the sixth ligand was assigned as a terminal oxo, and in subsequent structures of NapAB from E. coli and R. sphaeroides the sixth ligand to the oxidized molybdenum center was viewed as a coordinated water or hydroxo ligand.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The revised crystal structure of D. desulfuricans NapA and the structures of C. necator show no terminal oxo-group.

    “The revised crystal structure of D. desulfuricans NapA and the structures of C. necator show no terminal oxo-group.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [120] Najmudin S Gonzalez PJ Trincao J Coelho C Mukhopadhyay A Cerqueira NMFSA Romao CC Moura I Moura JJG Brondino CD Romao MJ JBIC, J. Biol. Inorg. Chem 2008 13 737 753 18327621

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    OAT reactivity has been observed in discrete inorganic molecules, as well as in proton coupled electron transfer reactions.

    “such OAT reactivity has been observed in discrete inorganic molecules,144,161,173,190–194 as well as the proton coupled electron transfer reactions.173–175,177,195–197”
    Quote in the paperNot a substantial claim0 of 10 sources checked
    • cites [144] Lim BS Holm RH J. Am. Chem. Soc 2001 123 1920 1930 11456813

      Not checked in the free run.

    • cites [161] Enemark JH Cooney JJA Wang J-J Holm RH Chem. Rev 2004 104 1175 1200 14871153

      Not checked in the free run.

    • cites [173] Nemykin VN Davie SR Mondal S Rubie N Kirk ML Somogyi A Basu P J. Am. Chem. Soc 2002 124 756 757 11817943

      Not checked in the free run.

    • cites [190] Jiang J Holm RH Inorg. Chem 2005 44 1068 1072 15859288

      Not checked in the free run.

    • cites [191] Wang J-J Tessier C Holm RH Inorg. Chem 2006 45 2979 2988 16562954

      Not checked in the free run.

    • cites [192] Sugimoto H Tatemoto S Suyama K Miyake H Mtei RP Itoh S Kirk ML Inorg. Chem 2010 49 5368 5370 20491454 PMC4020915

      Not checked in the free run.

    • cites [193] Donahue JP Goldsmith CR Nadiminti U Holm RH J. Am. Chem. Soc 1998 120 12869 12881

      Not checked in the free run.

    • cites [194] Majumdar A Sarkar S Coord. Chem. Rev 2011 255 1039 1054

      Not checked in the free run.

    • cites [174] Dutta SK McConville DB Youngs WJ Chaudhury M Inorg. Chem 1997 36 2517 2522

      Not checked in the free run.

    • cites [175] Laughlin LJ Young CG Inorg. Chem 1996 35 1050 1058 11666284

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In the oxidized state of D. desulfuricans NapA and C. necator, a sulfido group was found; in the reduced state, a persulfide bond between the sulfido sulfur and the cysteine sulfur was found.

    “Instead a sulfido group was found in the oxidized state and in the reduced state a persulfide bond between the sulfido sulfur and the cysteine sulfur.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [120] Najmudin S Gonzalez PJ Trincao J Coelho C Mukhopadhyay A Cerqueira NMFSA Romao CC Moura I Moura JJG Brondino CD Romao MJ JBIC, J. Biol. Inorg. Chem 2008 13 737 753 18327621

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The persulfide bond was viewed under dynamic control that generates an oxygen-sulfido intermediate and a sulfido species under turnover conditions, in both cases the coordinated cysteine comes off of the Mo-center.

    “Specifically, the persulfide bond was viewed under dynamic control that generates an oxygen-sulfido intermediate and a sulfido species under turnover conditions, in both cases the coordinated cysteine comes off of the Mo-center.120,121,201”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [120] Najmudin S Gonzalez PJ Trincao J Coelho C Mukhopadhyay A Cerqueira NMFSA Romao CC Moura I Moura JJG Brondino CD Romao MJ JBIC, J. Biol. Inorg. Chem 2008 13 737 753 18327621

      Not checked in the free run.

    • cites [121] Coelho C Gonzalez PJ Moura JG Moura I Trincao J Romao MJ J. Mol. Biol 2011 408 932 948 21419779

      Not checked in the free run.

    • cites [201] Gonzalez PJ Rivas MG Mota CS Brondino CD Moura I Moura JJG Coord. Chem. Rev 2013 257 315 331

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Initial crystal structures of DMSO reductase showed different geometries about the Mo-center due to sample heterogeneity as revealed by a high resolution structure coupled with spectroscopic investigations.

    “initial crystal structures of DMSO reductase showed different geometries about the Mo-center due to sample heterogeneity as revealed by a high resolution structure coupled with spectroscopic investigations.118,204”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [118] Pushie MJ George GN Coord. Chem. Rev 2011 255 1055 1084

      Not checked in the free run.

    • cites [204] Cotelesage JJH Pushie MJ Grochulski P Pickering IJ George GN J. Inorg. Biochem 2012 115 127 137 22824156

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Previous EXAFS studies of Nap have pointed out the presence of a terminal oxo group.

    “previous EXAFS studies of Nap have pointed out the presence of a terminal oxo group.206”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [206] Butler CS Charnock JM Garner CD Thomson AJ Ferguson SJ Berks BC Richardson DJ Biochem. J 2000 352 859 864 11104696 PMC1221527

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In the case of DMSOR, the enzyme is functional with Mo or W.

    “In the case of DMSOR, the enzyme is functional with Mo or W.207”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [207] Stewart LJ Bailey S Bennett B Charnock JM Garner CD McAlpine AS J. Mol. Biol 2000 299 593 600 10835270

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Monovalent cations (e.g., potassium and sodium) have a stimulatory effect on D. desulfuricans NapA activity, while divalent cations (e.g., magnesium and calcium) have an inhibitory effect.

    “Monovalent cations (e.g., potassium and sodium) have a stimulatory effect, while divalent cations (e.g., magnesium and calcium) have an inhibitory effect.210”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [210] Bursakov SA Carneiro C Almendra MJ Duarte RO Caldeira J Moura I Moura JJG Biochem. Biophys. Res. Commun 1997 239 816 822 9367852

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Both ferricyanide and cyanide are inhibitors of D. desulfuricans NapA; however, the presence of phosphate neutralizes the inhibition by cyanide at a lower concentration.

    “Both ferricyanide and cyanide are inhibitors; however, the presence of phosphate neutralizes the inhibition by cyanide at a lower concentration.210”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [210] Bursakov SA Carneiro C Almendra MJ Duarte RO Caldeira J Moura I Moura JJG Biochem. Biophys. Res. Commun 1997 239 816 822 9367852

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The W-containing nitrate reductase from Pyrobaculum aerophilum has a very high specific activity (Kcat 1162 s−1 and Km 58 μM) and functions optimally at a temperature greater than 95 °C.

    “It has a very high specific activity (Kcat 1162 s−1 and Km 58 µM) and functions optimally at a temperature greater than 95 °C.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [208] Afshar S Johnson E de Vries S Schröder I J. Bacteriol 2001 183 5491 5495 11544209 PMC95438

      Not checked in the free run.

  • The quote only partly states this claim.

    Premisecitation

    The optimal pH for nitrate reduction by D. desulfuricans NapA was found to be 8.

    “The optimal pH for nitrate reduction was found to be 8.211”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [211] Bursakov S Liu M-Y Payne WJ LeGall J Moura I Moura JJG Anaerobe 1995 1 55 60 16887508

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Thiocyanate inhibition of Paracoccus pantotrophus NapA occurs with direct binding to the Mo-center and subsequent displacement of one pyranopterin cofactor.

    “Thiocyanate inhibition occurs with direct binding to the Mo-center and subsequent displacement of one pyranopterin cofactor.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [206] Butler CS Charnock JM Garner CD Thomson AJ Ferguson SJ Berks BC Richardson DJ Biochem. J 2000 352 859 864 11104696 PMC1221527

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In the reduced state the calculated Kd for the NapAB complex is ~0.5 nM, while that in the oxidized state is 2.4 μM.

    “In the reduced state the calculated Kd is ~0.5 nM while that in the oxidized state is 2.4 µM.186”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [186] Arnoux P Sabaty M Alric J Frangioni B Guigliarelli B Adriano J-M Pignol D Nat. Struct. Biol 2003 10 928 934 14528294 source

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    In general, Nap enzymes have a high affinity for nitrate, with micromolar Km values (less than 300 μM), and a Vmax ~2 μmol min−1 mg−1.

    “In general, Nap enzymes have a high affinity for nitrate (Table 5), with micromolar Km values (less than 300 µM), and a Vmax ~2 µmol min−1 mg−1.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Removal of NapB from the NapAB complex reduces the efficiency of the monomer only 4-6 fold in R. sphaeroides but 30 fold in Thiosphaera pantotropha.

    “Removal of NapB from the NapAB complex reduces the efficiency of the monomer only 4–6 fold in R. sphaeroides186 but 30 fold in Thiosphaera pantotropha.214”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [186] Arnoux P Sabaty M Alric J Frangioni B Guigliarelli B Adriano J-M Pignol D Nat. Struct. Biol 2003 10 928 934 14528294 source

      Not checked in the free run.

    • cites [214] Bennett B Berks BC Ferguson SJ Thomson AJ Richardson DJ Eur. J. Biochem 1994 226 789 798 7813468 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The catalytic activity of the R. sphaeroides NapAB complex is close to the reduction potential of the nitrate-saturated Mo(v/iv) couple even under non-saturating substrate conditions, suggesting strong substrate binding.

    “Frangioni et al. reported that the catalytic activity of the R. sphaeroides NapAB complex exhibits catalytic activity close to the reduction potential of the nitrate saturated Mo(v/iv) couple even under non-saturating substrate conditions suggesting a strong binding of the substrate.221”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [221] Frangioni B Arnoux P Sabaty M Pignol D Bertrand P Guigliarelli B Leger C J. Am. Chem. Soc 2004 126 1328 1329 14759176

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Under turnover conditions, the Nap enzyme has two forms, active and inactive, which interconvert on a time scale slower than catalytic turnover.

    “Under turnover conditions, the enzyme has two forms – active and inactive, and they interconvert on a time scale slower than the catalytic turnover.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [205] Fourmond V Sabaty M Arnoux P Bertrand P Pignol D Leger C J. Phys. Chem. B 2010 114 3341 3347 20163092

      Not checked in the free run.

    • cites [220] Fourmond V Burlat B Dementin S Sabaty M Arnoux P Etienne E Guigliarelli B Bertrand P Pignol D Leger C Biochemistry 2010 49 2424 2432 20146468

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    Different variables such as pH, substrate and electron source can influence the mechanism of Nap.

    “There are different variables such as pH, substrate and electron source that can influence the mechanism.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    The exact molecular nature of the components of the redox switch in either Nar or Nap is not clear at this time.

    “The exact molecular nature of the components of the redox switch in either enzyme is not clear at this time; it represents catalytically competent but kinetically distinct forms of the enzymes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Noninnocent behavior of coordinated sulfur involving internal redox has been reported in discrete inorganic compounds.

    “Noninnocent behavior of the coordinated sulfur involving internal redox has been reported in discrete inorganic compounds.223–231”
    Quote in the paperNot a substantial claim0 of 9 sources checked
    • cites [223] Doonan CJ Nielsen DJ Smith PD White JM George GN Young CG J. Am. Chem. Soc 2006 128 305 316 16390160

      Not checked in the free run.

    • cites [224] Eagle AA Laughlin LJ Young CG Tiekink ERT J. Am. Chem. Soc 1992 114 9195 9197

      Not checked in the free run.

    • cites [225] Harmer MA Halbert TR Pan WH Coyle CL Cohen SA Stiefel EI Polyhedron 1986 5 341 347

      Not checked in the free run.

    • cites [226] Llusar R Polo V Velez E Vicent C Inorg. Chem 2010 49 8045 8055 20695430

      Not checked in the free run.

    • cites [227] Thomas S Eagle AA Sproules SA Hill JP White JM Tiekink ERT George GN Young CG Inorg. Chem 2003 42 5909 5916 12971759

      Not checked in the free run.

    • cites [228] Wang K McConnachie JM Stiefel EI Inorg. Chem 1999 38 4334 4341 11670869

      Not checked in the free run.

    • cites [229] McConnachie CA Stiefel EI Inorg. Chem 1999 38 964 972 11670869

      Not checked in the free run.

    • cites [230] Coucouvanis D Adv. Inorg. Chem 1998 45 1 73

      Not checked in the free run.

    • cites [231] Mayer JM Chemtracts 1997 10 350 353

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The activity of the P. pantotrophus NapAB complex is linked to a single protonation event with a pKa = 7.8, and the enzyme exhibits a higher catalytic current at pH~6.

    “In this case, the activity of the complex has been linked to a single protonation event with a pKa = 7.8; the enzyme exhibits a higher catalytic current at pH~6.222”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [222] Gates AJ Richardson DJ Butt JN Biochem. J 2008 409 159 168 17900239

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    The g1 value in the "very high-g" species is greater than 2, suggesting substantial sulfur contributions in the SOMO.

    “The g1 value in “very high-g” is greater than 2 suggesting substantial sulfur contributions in the singly occupied molecular orbital (SOMO).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The "high-g" species has a gav ~ 1.99 and is also known as 'high-g split' or 'high-g resting' signal.

    “Perhaps the most common signal is the so-called “high-g” species with a gav ~ 1.99, also known as ‘high-g split’ or ‘high-g resting’ signal.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The EPR signals of the Mo-center in Nap have been designated into three broad categories based on their average g values: "very high-g", "low-g" and "high-g" species, and all are rhombic.

    “The EPR signals of the Mo-center in Nap have been designated into three broad categories based on their average g values (〈g〉). These are “very high-g”, “low-g” and “high-g” species (Table 6), and all of them are rhombic in nature.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    Anisotropic EPR spectra can be obtained at liquid nitrogen temperature (77 K).

    “Anisotropic EPR spectra can be obtained at liquid nitrogen temperature (77 K).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    A weakness of pulsed EPR is that other relevant states are not probed.

    “The same can also be viewed as a weakness, as other relevant states are not probed.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The g-factor of Mo(v) EPR falls within a narrow range of 1.8-2.2 and is sensitive to small geometric perturbations.

    “The g-factor falls within a narrow range of 1.8–2.2, yet it is sensitive to small geometric perturbations.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    EPR spectra of Mo(v) are normally observable at room temperature due to its long electronic relaxation time.

    “EPR spectra of Mo(v) are normally observable at room temperature due to its long electronic relaxation time of Mo(v).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    In most reported EPR studies of nitrate reductases, including periplasmic nitrate reductases, the g-values but not the molybdenum hyperfine constants (A-values) are reported.

    “In most cases, however, the g-values but not the molybdenum hyperfine constants (i.e., A-values), are reported.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Because of the narrow line-width of Mo(v) signals, small hyperfine coupling due to interaction with other magnetic nuclei such as hydrogen and phosphorus can be observed in CW EPR spectra either directly or by difference spectroscopy.

    “Because of the narrow line-width of the Mo(v) signals, small hyperfine coupling due to the interaction with other magnetic nuclei such as hydrogen and phosphorus, can be observed in CW EPR spectra either directly or by difference spectroscopy.235,242”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [235] Bray RC Lowe DJ Biochem. Soc. Trans 1997 25 762 768 9388541

      Not checked in the free run.

    • cites [242] George GN Bray RC Morpeth FF Boxer DH Biochem. J 1985 227 925 931 2988508 PMC1144923

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    The naturally abundant stable molybdenum isotopes (95Mo, 97Mo) give rise to characteristic and unique EPR signals for Mo(v).

    “The naturally abundant, stable molybdenum isotopes (95Mo, I = 5/2, 15.72%; 97Mo, I = 5/2, 9.46% and I = 0 isotopes, 74.82%) give rise to characteristic and unique EPR signals for Mo(v).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The "very high-g" species is considered to originate from an inactive form of the enzyme.

    “This “very high-g” species is considered to originate from an inactive form of the enzyme.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The "high-g" signal does not represent a catalytically competent species due to its insensitivity to pH and other ligands (nitrate, nitrite, cyanide, azide, and thiocyanate).

    “It has been suggested that this signal does not represent a catalytically competent species due to its insensitivity to pH and other ligands (i.e., nitrate, nitrite, cyanide, azide, and thiocyanate). 206,212”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [206] Butler CS Charnock JM Garner CD Thomson AJ Ferguson SJ Berks BC Richardson DJ Biochem. J 2000 352 859 864 11104696 PMC1221527

      Not checked in the free run.

    • cites [212] Butler CS Charnock JM Bennett B Sears HJ Reilly AJ Ferguson SJ Garner CD Lowe DJ Thomson AJ Berks BC Richardson DJ Biochemistry 1999 38 9000 9012 10413473

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The nuclear gyromagnetic ratios of the two I=5/2 Mo isotopes are very similar, and their signals are normally indistinguishable in continuous wave EPR spectroscopy.

    “The nuclear gyromagnetic ratios of the two isotopes with I = 5/2 are very similar to one another, and the signals originating from the two isotopes are normally indistinguishable in continuous wave EPR spectroscopy.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisereasoning

    The "low-g" signal (gav ~ 1.96) is observed when the enzyme is incubated with dithionite, reminiscent of the XO signal, suggesting the presence of only one dithiolene moiety, as in XO or SO.

    “The “low-g” (gav ~ 1.96) is observed when the enzyme is incubated with dithionite, reminiscent of the XO signal. Thus, it suggests the presence of only one dithiolene moiety, as is the case for XO or SO.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    An isotropic Mo(v) EPR signal consists of one large central peak (~75% of total intensity) with 6 satellite peaks (~25% of total intensity).

    “Thus, an isotropic Mo(v) EPR signal consists of one large central peak (~75% of total intensity) with 6 satellite peaks (~25% of total intensity).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    The genes in the nap operon can be divided into two groups, redox active or maturation, based on the physiological functions of the translated proteins.

    “The genes in the nap operon can be divided into two groups, redox active or maturation, based on the physiological functions of the translated proteins.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Biaso et al. suggest a MoS6 core, and different species arise due to the presence of different ions and/or a structure distortion.

    “What they suggest is a MoS6 core, and different species arise due to the presence of different ions, and/or a structure distortion.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [248] Biaso F Burlat B Guigliarelli B Inorg. Chem 2012 51 3409 3419 22397692

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Of the Nap EPR species, the 'high-g' species is a more reduced state where the disulfide bond is reduced, while the 'low-g' signal is attributed to a species coordinated by only one pterin cofactor.

    “Of these, the ‘high-g’ species is a more reduced state where the disulfide bond is reduced, while the ‘low-g’ signal is attributed to a species coordinated by only one pterin cofactor, as proposed before.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    The presence of auxiliary nap genes varies among organisms, and no solitary nap gene can be considered ubiquitous to all napA encoding organisms.

    “The presence of these genes varies among organisms and no solitary nap gene can be considered ubiquitous to all napA encoding organisms.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Subsequent experiments with reduced viologen showed the 'high-g' signal during catalysis, raising questions about the 'high-g nitrate' signal.

    “However, subsequent experiments with reduced viologen showed the ‘high-g’ signal during catalysis raising questions about the ‘high-g nitrate’ signal.245”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [245] Butler CS Fairhurst SA Ferguson SJ Thomson AJ Berks BC Richardson DJ Lowe DJ Biochem. J 2002 363 817 823 11964184 PMC1222536

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Biaso et al. considered different 'high-g' signals - 'high g-resting', 'high-g nitrate' and 'high-g turnover' to be magnetically similar, indicating little difference in the first coordination sphere.

    “Biaso et al. considered different ‘high-g’ signals – ‘high g-resting’, ‘high-g nitrate’ and ‘high-g turnover’ to be magnetically similar to each other indicating little difference in the first coordination sphere.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [248] Biaso F Burlat B Guigliarelli B Inorg. Chem 2012 51 3409 3419 22397692

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Under turnover conditions using dithionite as a reductant, a signal called 'high-g nitrate' with lower anisotropy has been reported.

    “Under turnover conditions using dithionite as a reductant, another signal called ‘high-g nitrate’ with a lower anisotropy has been reported.206,212”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [206] Butler CS Charnock JM Garner CD Thomson AJ Ferguson SJ Berks BC Richardson DJ Biochem. J 2000 352 859 864 11104696 PMC1221527

      Not checked in the free run.

    • cites [212] Butler CS Charnock JM Bennett B Sears HJ Reilly AJ Ferguson SJ Garner CD Lowe DJ Thomson AJ Berks BC Richardson DJ Biochemistry 1999 38 9000 9012 10413473

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A tyrosine residue in NapA is conserved in all heterodimeric NapA proteins and absent in monomeric NapA proteins such as D. desulfuricans.

    “This tyrosine residue is conserved in all heterodimeric NapA proteins and absent in monomeric NapA proteins such as D. desulfuricans.188”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [188] Jepson BJN Marietout A Mohan S Cole JA Butler CS Richardson DJ Biochem. Soc. Trans 2006 36 122 126 16417499

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    C. jejuni encodes a large variety of genes associated with iron scavenging, uptake, and storage, one of which (chu) can transport intact heme into the cell.

    “C. jejuni encodes a large variety of genes associated with iron scavenging, uptake, and storage, one of which (chu) can transport intact heme into the cell.256”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [256] Wooldridge KG van Vlietn AHM Konkel ME Ketley JM Campylobacter: molecular and cellular biology 2005 Wymondham, UK Horizon Scientific Press

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The N- and C-termini of NapB are poorly conserved and are not involved in electron transfer to NapA.

    “The N- and C-termini are poorly conserved, and are not involved in electron transfer to NapA.251”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [251] Brigé A Leys D Meyer TE Cusanovich MA Van Beeumen JJ Biochemistry 2002 41 4827 4836 11939777

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Crystal structures of two monomeric NapAs are available.

    “Additionally, the crystal structures of two monomeric NapAs are available.96,119”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [96] Jepson BJN Mohan S Clarke TA Gates AJ Cole JA Butler CS Butt JN Hemmings AM Richardson DJ J. Biol. Chem 2007 282 6425 6437 17130127

      Not checked in the free run.

    • cites [119] Dias J Than M Humm A Bourenkov GP Bartunik HD Bursakov S Calvete J Caldeira J Carneiro C Moura JJ Moura I Romao MJ Structure 1999 7 65 79 10368307

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Rhodobacter sphaeroides and Cupriavidus necator NapAB heterodimer structures have been determined using X-ray crystallography.

    “The Rhodobacter sphaeroides and Cupriavidus necator NapAB heterodimer structures have been determined using X-ray crystallography.121,186”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [121] Coelho C Gonzalez PJ Moura JG Moura I Trincao J Romao MJ J. Mol. Biol 2011 408 932 948 21419779 source

      Not checked in the free run.

    • cites [186] Arnoux P Sabaty M Alric J Frangioni B Guigliarelli B Adriano J-M Pignol D Nat. Struct. Biol 2003 10 928 934 14528294 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The ccmABC-DEFGHI operon is located directly adjacent to the nap operon in E. coli, but this is not the situation in most other organisms.

    “While the ccmABC-DEFGHI operon is located directly adjacent to the nap operon in E. coli,255 this is not the situation in most other organisms.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [255] Stewart V Lu Y Darwin AJ J. Bacteriol 2002 184 1314 1323 11844760 PMC134854

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The ability of C. jejuni to utilize intact heme could make cytochrome c biogenesis redundant and thus energetically unfavorable.

    “The ability of C. jejuni to utilize intact heme could make cytochrome c biogenesis redundant, and thus energetically unfavorable.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    NapC belongs to the NapC/NirT family of tetraheme proteins.

    “NapC belongs to a large group of tetra heme proteins, the NapC/NirT family.259”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [259] Gross R Eichler R Simon J Biochem. J 2005 390 689 693 15907193 PMC1199662

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    napD is an essential component of nitrate reduction; in all napD mutants nitrate reduction is inhibited.

    “The R. sphaeroides, E. coli, and W. succinogenes mutational studies are in agreement, napD is an essential component of nitrate reduction, as in all napD mutants nitrate reduction is inhibited.102,105,215”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [102] Potter LC Cole JA Biochem. J 1999 344 69 76 10548535 PMC1220615

      Not checked in the free run.

    • cites [105] Kern M Mager AM Simon J Microbiology 2007 153 3739 3747 17975082

      Not checked in the free run.

    • cites [215] Reyes F Gavira M Castillo F Moreno-Vivián C Biochem. J 1998 331 897 904 9560320 PMC1219433

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    NapG contains four iron sulfur binding motifs and is associated with the periplasmic face of the membrane.

    “NapG contains four iron sulfur binding motifs and is associated with the periplasmic face of the membrane.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    NapH is an integral membrane protein whose cytoplasmic portion contains two iron sulfur binding motifs.

    “NapH is an integral membrane protein. The cytoplasmic portion of NapH contains two iron sulfur binding motifs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisenone given

    Campylobacter only has menaquinone but does not have a NapC homologue.

    “Campylobacter only has menaquinone, but does not have a NapC homologue.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Neither Photobacterium damselae nor Rhodothermus marinus is capable of reducing nitrate despite having a napA homologue.

    “For example, neither Photobacterium damselae,270 or Rhodothermus marinusas271 are capable of reducing nitrate despite having a napA homologue.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [270] Thyssen A Grisez L Van Houdt R Ollevier F Int. J. Syst. Bacteriol 1998 48 1145 1151 9828416 source

      Not checked in the free run.

    • cites [271] Alfredsson GA Kristjansson JK Hjorleifsdottir S Stetter KO J. Gen. Microbiol 1988 134 299 306

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    NapD lacks a conserved NapA binding motif.

    “NapD lacks a conserved NapA binding motif.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Mutation of napF does not completely abolish nitrate reductase activity in E. coli, but a drastic decrease in activity is observed in R. sphaeroides and W. succinogenes.

    “While mutation of the napF gene does not completely abolish nitrate reductase activity in E. coli,102 a drastic decrease in activity is observed in R. sphaeroides and W. succinogenes.105,215”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [102] Potter LC Cole JA Biochem. J 1999 344 69 76 10548535 PMC1220615

      Not checked in the free run.

    • cites [105] Kern M Mager AM Simon J Microbiology 2007 153 3739 3747 17975082

      Not checked in the free run.

    • cites [215] Reyes F Gavira M Castillo F Moreno-Vivián C Biochem. J 1998 331 897 904 9560320 PMC1219433

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    Sorangium cellulosum and Anaeromyxobacter species can reduce nitrate, but this activity cannot be attributed to NapA without more detailed investigation because their genomes encode multiple nitrate reductases.

    “Sorangium cellulosum and Anaeromyxobacter species can reduce nitrate,272,273 though this activity cannot be attributed to NapA without a more detailed investigation as the genomes of these organisms encode multiple nitrate reductases (i.e., Nar, Nap and Nas).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [272] Knauber T Doss SD Gerth K Perlova O Müller R Treuner-Lange A Mol. Microbiol 2008 69 254 266 18513216

      Not checked in the free run.

    • cites [273] Sanford RA Cole JR Tiedje JM Appl. Environ. Microbiol 2002 68 893 900 11823233 PMC126698

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    NapL is found primarily in the Epsilonproteobacteria.

    “A third putative maturation protein, NapL, is found primarily in the Epsilonproteobacteria.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    NapF is not considered essential for NapA maturation, although it aids in [4Fe-4S] insertion.

    “NapF is not considered to be essential for NapA maturation, although it does aid in [4Fe–4S] insertion. 105,258,274”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [105] Kern M Mager AM Simon J Microbiology 2007 153 3739 3747 17975082 source

      Not checked in the free run.

    • cites [258] Brondijk TH Fiegen D Richardson DJ Cole JA Mol. Microbiol 2002 44 245 255 11967083 source

      Not checked in the free run.

    • cites [274] Nilavongse A Brondijk THC Overton TW Richardson DJ Leach ER Cole JA Microbiology 2006 152 3227 3237 17074894 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The gene napL encodes a 35 kDa periplasmic chaperone protein with no known metal binding motifs.

    “The gene napL encodes a 35 kDa periplasmic chaperone protein,103,105 with no known metal binding motifs.103”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [103] Kern M Simon J Microbiology 2009 155 2784 2794 19477904 source

      Not checked in the free run.

    • cites [105] Kern M Mager AM Simon J Microbiology 2007 153 3739 3747 17975082 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    NifL is the redox sensor domain of the NifLF two-component regulatory system, which along with NifA regulates nitrogen fixation genes in response to oxygen.

    “NifL is the redox sensor domain of the NifLF two-component regulatory system, which, along with NifA, regulates nitrogen fixation genes in response to oxygen. 277,278”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [277] Dixon R Kahn D Nat. Rev. Microbiol 2004 2 621 631 15263897

      Not checked in the free run.

    • cites [278] Martinez-Argudo I Little R Shearer N Johnson P Dixon R J. Bacteriol 2004 186 601 610 14729684 PMC321506

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisenone given

    The napS gene is annotated as a methyl-accepting chemotaxis sensor protein, part of the PAS superfamily.

    “The napS gene, found in Arcobacter butzleri (YP_001489295.1 or ZP_07891038.1), Sulfurovum sp. (YP_004049825.1), Nitratiruptor sp. SB155-2 (YP_001357263.1) and Sulfurimonas denitrificans (YP_003892305.1), is annotated as a methyl-accepting chemotaxis sensor protein, part of the PAS (Per-ARNT-Sim) superfamily.”
    Quote in the paperNot a substantial claim
120 of 120

  • The paper relies on this without support.

    The pterin cofactor adopts different geometries depending on its redox state, and these differences are manifested in torsion angles.

    “The pterin cofactor is expected to adopt different geometries depending on the redox state, and these differences are manifested in their torsion angles.”

  • The paper relies on this without support.

    For most crystallographically determined structures, the <OCCS and <OCCC torsion angles reflect the intrinsic geometry of the pterin cofactor rather than artifacts of structure quality.

    “For most structures, the angles linearly correlate with the exception of a few DMSOR and formate dehydrogenase (FDH) structures that may reflect the quality of the structure rather than an intrinsic property of the cofactor.”

  • The authors state this as an assumption.

    The internal redox chemistry of sulfur is operative under low nitrate loading.

    “This mechanism takes advantage of the internal redox chemistry of sulfur and assumes that it is operative under low nitrate loading.”

  • The paper relies on this without support.

    The presence of a nap gene in a genome indicates that the organism can express a functional protein for that role.

    “The presence of NapC and/or NapH may be an indication that the organism can catalyze nitrate respiration via Nap.”

  • The paper relies on this without support.

    Sequence homology to a structurally characterized protein indicates functional similarity.

    “The putative NapS proteins exhibit significant homology with the structurally characterized region of Azotobacter vinelandii NifL.”
5 of 5

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Figure 15 is identified as both a NapD structure and a NapA tree

    Minor

    The text associates Fig. 15 with the structure and binding of NapD, but later calls it the NapA phylogenetic tree.

  • Figure 18 is identified as both an electron-transfer pathway and a phylogenetic tree

    Minor

    The text assigns two different subjects to Fig. 18: an electron-transfer pathway and a NapA sequence tree.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 15

  1. CRC, ed. D. Lide, CRC Press, Cleveland, OH, 75 edn, 1994–1995, pp. 5–16, 15–20
  2. Moga, 2013, J. Environ. Prot. Ecol., 14, 341
  3. Allison, 1988, J. Gen. Microbiol., 134, 1397
  4. Kelly, 2013, Am. J. Physiol., 304, R73
  5. Gladwin, 2006, Am. J. Physiol.: Heart Circ. Physiol., 291, H2026
  6. Mayer, 1997, Chemtracts, 10, 350
  7. R. C. Bray , Flavins Flavoproteins, Proc. Int. Symp., 1984
  8. Alfredsson, 1988, J. Gen. Microbiol., 134, 299
  9. Teixidó, 2010, Int. Microbiol., 13, 33
  10. Kumar, 1999, Am. J. Physiol., 276, R265
  11. T. Mussini and P.Longhi, The Halogens: Chlorine, Marcel Dekker, Inc, New York, 1985
  12. A. F. W. M. Wolterink , Wageningen University, PhD thesis, 2004
  13. S. I. Zhdanov , in Standard Potentials in Aquesous Solution, ed. A. J. Bard, R. Parsons and J. Jordan, Marcel Dekker, New York, 1985, pp. 93–125
  14. Z. Galus , in Standard Potentials in Aqueous Solution, ed. A. J. Bard, R. Parsons and J. Jordan, Mercel Dekker, New York, 1985, pp. 189–235
  15. N. W. H. Cheetham , Introducing Biological Energetics, Oxford University Press, New York, 2011

Cited by

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Related

Authors
Sparacino-Watkins, C., Stolz, J. F., & Basu, P.
Affiliations
Duquesne University (US)
Corresponding author
Basu, Partha
ORCID
Venue
Chem. Soc. Rev.
Publisher
Royal Society of Chemistry (RSC)
Published
2014
Volume
43
Issue
2
Pages
676-706
ISSN
  • 0306-0012 (ISSN-L)
  • 1460-4744
DOI
10.1039/c3cs60249d
PMC
PMC4080430
OpenAlex
W2063700392
Semantic Scholar
1a41e55b2b20d71c4ca485cdad3ff30e6efd778b
Cited by
426
References
338
Citations by year
2026: 54 · 2025: 79 · 2024: 44 · 2023: 36 · 2022: 35 · 2021: 45 · 2020: 30 · 2019: 24 · 2018: 21 · 2017: 17 · 2016: 12 · 2015: 16 · 2014: 11 · 2012: 1
FWCI
0.73
Type
journal article
Language
en
Open access
Locations
  • Chemical Society Reviews (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (R15GM061555)
Topics
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Physical Sciences › Environmental Science › Pollution › Wastewater Treatment and Nitrogen Removal
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
periplasmic nitrate reductase, NAP, nitrate reduction, respiratory nitrate reductase, assimilatory nitrate reductase, nitrogen cycling, Proteobacteria, phylogenetic relationships, operon structure, redox chemistry, enzyme kinetics, auxiliary proteins, dissimilatory nitrate reduction, nitrate assimilation
MeSH terms
Bacterial Proteins, Gram-Negative Bacteria, Gram-Positive Bacteria, Humans, Models, Molecular, Nitrate Reductases, Nitrates, Operon, Oxidation-Reduction, Phylogeny, Gene Expression Regulation, Bacterial, Periplasm, Catalytic Domain, Proteobacteria, Nitrogen Cycle

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

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