CoChat
Sign Up
PreprintCited by 10Enzyme Structure and FunctionMetalloenzymes and iron-sulfur proteinsProtein Structure and Dynamics

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins

Open access
Kahle, Maximilian, Appelgren, Sofia, Elofsson, Arne, Carroni, Marta, Ädelroth, Pia·2022·BMC Biology
DOI 10.1101/2022.11.16.516607PMC PMC9976466

Preprint — published as 10.1186/s12915-023-01546-w · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (Fe B ) cofactor insertion into cytochrome c -dependent nitric oxide reductase ( c NOR). c NOR catalyzes the NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed Fe B insertion, and the general mechanism of the MoxR/VWA interacting protein families. We show that NorQ-catalyzed ATP hydrolysis, an intact VWA-domain in NorD and specific surface carboxylates on c NOR are all features required for c NOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that ‘plugs’ the NorQ ring pore to the VWA domain of NorD with a protruding ‘finger’ inserting through the pore, and suggest this binding mode to be general for MoxR/VWA couples. We present a tentative model for the mechanism of NorQD-catalyzed c NOR remodelling and suggest many of its features to be applicable to the whole MoxR/VWA family.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2022.11.16.516607

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

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

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 71

  1. 10.1038/nrmicro2057 · DOI
  2. 2018, The insertion of the non-heme FeB cofactor into nitric oxide reductase from P. denitrificans depends on NorQ and NorD accessory proteins, Biochim. Biophys. Acta, 1859, 1051, 10.1016/j.bbabio.2018.05.020 · DOI
  3. 10.1007/400_2007_046 · DOI
  4. 10.1016/j.bbabio.2011.09.020 · DOI
  5. 10.1126/science.1195591 · DOI
  6. 10.1021/ja0016295 · DOI
  7. 10.1074/jbc.M201913200 · DOI
  8. 10.1021/bi0121050 · DOI
  9. 2007, A pathway for protons in nitric oxide reductase from Paracoccus denitrificans, Biochim. Biophys. Acta, 1767, 362, 10.1016/j.bbabio.2007.03.006 · DOI
  10. 10.1371/journal.pone.0019117 · DOI
  11. 10.1016/j.bbabio.2012.01.003 · DOI
  12. 10.1074/jbc.C500061200 · DOI
  13. 2016, Uncovering the Transmembrane Metal Binding Site of the Novel Bacterial Major Facilitator Superfamily-Type Copper Importer CcoA, mBio, 7, e01981
  14. 10.1111/j.1432-1033.1996.0592r.x · DOI
  15. 10.1023/A:1020547225398 · DOI
  16. 1997, Purification and initial kinetic and spectroscopic characterization of NO reductase from Paracoccus denitrificans, Biochim. Biophys. Acta, 1318, 202, 10.1016/S0005-2728(96)00138-7 · DOI
  17. 10.1016/j.jinorgbio.2004.09.024 · DOI
  18. 10.1016/0014-5793(92)81495-8 · DOI
  19. 2019, Insights into the mechanism of nitric oxide reductase from a FeB-depleted variant, FEBS Lett, 593, 1351, 10.1002/1873-3468.13436 · DOI
  20. 10.1016/j.jsb.2006.02.009 · DOI
  21. 10.1016/j.jsb.2012.03.010 · DOI
  22. 10.1186/gb-2008-9-4-216 · DOI
  23. 10.1038/s41580-019-0183-6 · DOI
  24. 10.1016/j.sbi.2020.10.027 · DOI
  25. 10.1073/pnas.1911123117 · DOI
  26. 2019, Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC, Nat. Commun, 10, 3058, 10.1038/s41467-019-11084-1 · DOI
  27. 10.1073/pnas.1009092107 · DOI
  28. 10.1007/s00018-016-2374-z · DOI
  29. 10.1091/mbc.E02-05-0259 · DOI
  30. 10.1016/j.jmb.2016.12.008 · DOI
  31. 10.1038/ncomms9883 · DOI
  32. 10.1371/journal.pone.0047424 · DOI
  33. 10.1038/srep16243 · DOI
  34. R. Evans et al., Protein complex prediction with AlphaFold-Multimer. bioRxiv 10.1101/2021.10.04.463034, 2021.2010.2004.463034 (2021). · DOI · Paper page
  35. 10.1038/s41594-019-0304-0 · DOI
  36. 2020, Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes, Nat. Commun, 11, 5907, 10.1038/s41467-020-19735-4 · DOI
  37. 10.1016/j.jsb.2013.08.010 · DOI
  38. 10.1016/S0959-440X(02)00388-3 · DOI
  39. 10.1016/j.cell.2009.09.034 · DOI
  40. 10.1038/ncomms9781 · DOI
  41. 10.1016/j.str.2016.03.001 · DOI
  42. 2019, Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation, Cell Rep, 26, 29, 10.1016/j.celrep.2018.12.037 · DOI
  43. 10.1073/pnas.1810648115 · DOI
  44. 2020, Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex, Commun. Biol, 3, 46, 10.1038/s42003-020-0772-0 · DOI
  45. 10.1074/jbc.RA119.011916 · DOI
  46. 2018, Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis, Cell, 175, 822, 10.1016/j.cell.2018.09.015 · DOI
  47. 10.1038/s41467-019-10922-6 · DOI
  48. S. Andrews et al. (2013) Control of iron metabolism in Bacteria. in Metal Ions in Life Sciences, pp 203–239. · DOI · Paper page
  49. 10.1128/JB.183.1.189-199.2001 · DOI
  50. 10.1006/bbrc.1998.9549 · DOI
  51. 10.1074/jbc.M704615200 · DOI
  52. U. Flock , Nitric Oxide Reductase from Paracoccus denitrificans-A proton transfer pathway from the ‘wrong’ side. Ph. D. thesis, Stockholm University, Stockholm (2008).
  53. 10.1016/0076-6879(88)56014-7 · DOI
  54. 10.1016/0003-2697(79)90115-5 · DOI
  55. 10.1074/jbc.M113.497347 · DOI
  56. 10.1016/S0076-6879(07)37005-5 · DOI
  57. 10.1139/v84-121 · DOI
  58. 10.1111/j.1432-1033.1992.tb16976.x · DOI
  59. 10.7554/eLife.42166 · DOI
  60. 10.1093/bioinformatics/btt429 · DOI
  61. 10.1038/nmeth.4169 · DOI · Paper page
  62. M. Mirdita , K. Schütze , Y. Moriwaki , L. Heo , S. Ovchinnikov , ColabFold - Making protein folding accessible to all PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-1032816/v1] (2021). · DOI · Paper page
  63. 10.1093/bioinformatics/btm098 · DOI · Paper page
  64. 10.1093/nar/gkaa1100 · DOI · Paper page
  65. 2020, MGnify: the microbiome analysis resource in 2020, Nucleic Acids Res, 48, D570
  66. 10.1371/journal.pcbi.1002195 · DOI · Paper page
  67. 10.1186/s12859-019-3019-7 · DOI · Paper page
  68. 10.1038/s41592-019-0437-4 · DOI · Paper page
  69. 10.1093/nar/gkw1081 · DOI
  70. 10.1093/nar/gki524 · DOI · Paper page
  71. 2022, Improved prediction of protein-protein interactions using AlphaFold2, Nat. Commun, 13, 1265, 10.1038/s41467-022-28865-w · DOI · Paper page

Metadata

Authors
Kahle, M., Appelgren, S., Elofsson, A., Carroni, M., & Ädelroth, P.
Affiliations
Stockholm University (SE)
Corresponding author
  • Kahle, Maximilian
  • Carroni, Marta
  • Ädelroth, Pia
ORCID
Venue
BMC Biology
Publisher
openRxiv
Published
2022-11-16
Volume
21
Issue
1
Pages
47-47
ISSN
1741-7007 (ISSN-L)
DOI
10.1101/2022.11.16.516607
PMC
PMC9976466
OpenAlex
W4322625116
Cited by
10
References
1
Citations by year
2026: 3 · 2025: 6 · 2024: 1
FWCI
0.74
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • BMC Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Kempe Foundation
  • Swedish e-Science Research Centre
  • Knut och Alice Wallenbergs Stiftelse
  • Universität Potsdam
  • Vetenskapsrådet (2015-04512, 2016-06301, 2019-04124, Berzelius-2021-29)
  • Kempestiftelserna
  • Stockholms Universitet
  • Science for Life Laboratory
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Metalloenzymes and iron-sulfur proteins
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
Nord, VWA domain, Paracoccus denitrificans, denitrification, ATP hydrolysis, protein complex structure, structure-function relationship, molecular chaperones
MeSH terms
AAA Proteins, Norethindrone, Paracoccus denitrificans, Structure-Activity Relationship, Molecular Chaperones

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.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review