Nickel-based Enzyme Systems

Ragsdale, Stephen W.

doi:10.1074/jbc.r900020200

Cited by 400Metalloenzymes and iron-sulfur proteinsMetal-Catalyzed Oxygenation MechanismsEnzyme Structure and Function

Nickel-based Enzyme Systems

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Ragsdale, Stephen W.·2009·Journal of Biological Chemistry

DOI 10.1074/jbc.r900020200PMC PMC2707248

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Abstract

Of the eight known nickel enzymes, all but glyoxylase I catalyze the use and/or production of gases central to the global carbon, nitrogen, and oxygen cycles. Nickel appears to have been selected for its plasticity in coordination and redox chemistry and is able to cycle through three redox states (1+, 2+, 3+) and to catalyze reactions spanning approximately 1.5 V. This minireview focuses on the catalytic mechanisms of nickel enzymes, with an emphasis on the role(s) of the metal center. The metal centers vary from mononuclear to complex metal clusters and catalyze simple hydrolytic to multistep redox reactions.

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Enzymes of core carbon and energy pathways in modern anaerobic autotrophs are replete with FeS, FeNiS and MoS (WS) centres.
“This is an important similarity to modern anaerobic autotrophs, whose enzymes of core carbon and energy pathways are replete with FeS, FeNiS and MoS (WS) centres, FeS and NiS usually being incorporated into proteins via cysteine residues [54–58], Mo and W usually being complexed by thiols of the molybdopterin cofactor MoCo [59].”
From Early bioenergetic evolution (2013) · cites this paper as [56]
The NiFe Hydrogenase and CO Dehydrogenase sections describe Fe-S clusters and nickel–iron centres in enzymes involved in anaerobic energy and carbon metabolism. They do not establish that such centres are widespread across modern anaerobic autotrophs, or address the claimed MoS (WS) centres. The supplied passages have no page numbers. (LLM, conf=0.86)
Experimental — accuracy not yet measured
In the enzymatic mechanism, electrons from a low-potential Fd reduce one molecule of CO2 to CO at the C cluster; the CO migrates to the A cluster, binds Ni at the Nip site; a methyl group from CoFeSP binds the same Ni atom; the carbonyl inserts to generate a Ni-bound acetyl group, which is removed via thiolysis by CoASH.
“In the enzymatic mechanism [56], electrons from a low-potential Fd are used by the enzyme to reduce one molecule of CO2 to CO at an FeNiS cluster called the C cluster; that CO migrates to a second FeNiS cluster in the enzyme (the A cluster), where it binds one of two Ni atoms at the Nip site to form a Ni-bound carbonyl group, where the two-electron donating property of Ni is important in the”
From Early bioenergetic evolution (2013) · cites this paper as [56]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
The catalysis in CODH/ACS is performed by transition metals Fe and Ni coordinated as sulfide clusters.
“The catalysis in CODH/ACS is performed by transition metals (Fe and Ni) coordinated as sulfide clusters [50,56,73].”
From Early bioenergetic evolution (2013) · cites this paper as [56]

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Authors: Ragsdale, S. W.
Affiliations: University of Michigan (US)
Corresponding author: Ragsdale, Stephen W.
ORCID: Ragsdale, Stephen W.
Venue: Journal of Biological Chemistry
Publisher: Elsevier BV
Published: 2009-07
Volume: 284
Issue: 28
Pages: 18571-18575
ISSN: 0021-9258 (ISSN-L)
DOI: 10.1074/jbc.r900020200
PMC: PMC2707248
OpenAlex: W1996983125
Cited by: 400
References: 40
Citations by year: 2026: 24 · 2025: 32 · 2024: 39 · 2023: 26 · 2022: 30 · 2021: 24 · 2020: 24 · 2019: 26 · 2018: 26 · 2017: 20 · 2016: 11 · 2015: 15 · 2014: 26 · 2013: 22 · 2012: 23
FWCI: 0.95
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
creativecommons.org/licenses/by/4.0/ (vor, 4138 d)
Locations: Journal of Biological Chemistry (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Funders: National Institute of General Medical Sciences (R01GM039451)
Topics: Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: nickel enzymes, nickel coordination chemistry, redox state, catalytic mechanism, metal centers, metal clusters, carbon cycle, nitrogen cycling, oxygen cycle, hydrolysis
MeSH terms: Acetate-CoA Ligase, Biochemistry, Carbon, Catalysis, Enzymes, Hydrogenase, Hydrolysis, Metals, Models, Molecular, Molecular Conformation, Nickel, Nitrogen, Oxidation-Reduction, Oxygen, Urease

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Nickel-based Enzyme Systems

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