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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1992 May 15;89(10):4427–4431. doi: 10.1073/pnas.89.10.4427

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

G O Tan 1, S A Ensign 1, S Ciurli 1, M J Scott 1, B Hedman 1, R H Holm 1, P W Ludden 1, Z R Korszun 1, P J Stephens 1, K O Hodgson 1
PMCID: PMC49095  PMID: 1584775

Abstract

The nickel/iron/sulfur center of the carbon monoxide dehydrogenase (carbon monoxide:(acceptor)oxidoreductase; EC 1.2.99.2) enzyme from Rhodospirillum rubrum (Rr-CODH) was studied by x-ray absorption spectroscopy at the Ni K edge. Extended x-ray absorption fine structure data show that the first Ni coordination shell consists of 2 S atoms at 2.23 A and 2-3 N/O atoms at 1.87 A. The edge structure indicates a distorted tetrahedral or five-coordinate Ni environment in both oxidized and reduced Rr-CODH. By comparing second-shell extended x-ray absorption fine structure data of Rr-CODH to that of (Et4N)3[NiFe3S4(SEt)4], a cubane-type cluster, it was clearly established that Ni in the Rr-CODH center is not involved in the core of a NiFe3S4 cubane cluster. One model consistent with the results is a mononuclear Ni2+ site, bridged by S-Cys or sulfide to one or both of the Fe4S4 clusters of the enzyme, with the remaining coordination sites occupied by additional S-Cys or N/O-liganding amino acid residues.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abbanat D. R., Ferry J. G. Synthesis of acetyl coenzyme A by carbon monoxide dehydrogenase complex from acetate-grown Methanosarcina thermophila. J Bacteriol. 1990 Dec;172(12):7145–7150. doi: 10.1128/jb.172.12.7145-7150.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bonam D., Ludden P. W. Purification and characterization of carbon monoxide dehydrogenase, a nickel, zinc, iron-sulfur protein, from Rhodospirillum rubrum. J Biol Chem. 1987 Mar 5;262(7):2980–2987. [PubMed] [Google Scholar]
  3. Bonam D., McKenna M. C., Stephens P. J., Ludden P. W. Nickel-deficient carbon monoxide dehydrogenase from Rhodospirillum rubrum: in vivo and in vitro activation by exogenous nickel. Proc Natl Acad Sci U S A. 1988 Jan;85(1):31–35. doi: 10.1073/pnas.85.1.31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bonam D., Murrell S. A., Ludden P. W. Carbon monoxide dehydrogenase from Rhodospirillum rubrum. J Bacteriol. 1984 Aug;159(2):693–699. doi: 10.1128/jb.159.2.693-699.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Diekert G. B., Thauer R. K. Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum. J Bacteriol. 1978 Nov;136(2):597–606. doi: 10.1128/jb.136.2.597-606.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Drake H. L., Hu S. I., Wood H. G. Purification of carbon monoxide dehydrogenase, a nickel enzyme from Clostridium thermocaceticum. J Biol Chem. 1980 Aug 10;255(15):7174–7180. [PubMed] [Google Scholar]
  7. Ensign S. A., Bonam D., Ludden P. W. Nickel is required for the transfer of electrons from carbon monoxide to the iron-sulfur center(s) of carbon monoxide dehydrogenase from Rhodospirillum rubrum. Biochemistry. 1989 Jun 13;28(12):4968–4973. doi: 10.1021/bi00438a010. [DOI] [PubMed] [Google Scholar]
  8. Ensign S. A., Campbell M. J., Ludden P. W. Activation of the nickel-deficient carbon monoxide dehydrogenase from Rhodospirillum rubrum: kinetic characterization and reductant requirement. Biochemistry. 1990 Feb 27;29(8):2162–2168. doi: 10.1021/bi00460a029. [DOI] [PubMed] [Google Scholar]
  9. Ensign S. A., Hyman M. R., Ludden P. W. Nickel-specific, slow-binding inhibition of carbon monoxide dehydrogenase from Rhodospirillum rubrum by cyanide. Biochemistry. 1989 Jun 13;28(12):4973–4979. doi: 10.1021/bi00438a011. [DOI] [PubMed] [Google Scholar]
  10. Grahame D. A., Stadtman T. C. Carbon monoxide dehydrogenase from Methanosarcina barkeri. Disaggregation, purification, and physicochemical properties of the enzyme. J Biol Chem. 1987 Mar 15;262(8):3706–3712. [PubMed] [Google Scholar]
  11. Krzycki J. A., Zeikus J. G. Characterization and purification of carbon monoxide dehydrogenase from Methanosarcina barkeri. J Bacteriol. 1984 Apr;158(1):231–237. doi: 10.1128/jb.158.1.231-237.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ragsdale S. W., Clark J. E., Ljungdahl L. G., Lundie L. L., Drake H. L. Properties of purified carbon monoxide dehydrogenase from Clostridium thermoaceticum, a nickel, iron-sulfur protein. J Biol Chem. 1983 Feb 25;258(4):2364–2369. [PubMed] [Google Scholar]
  13. Ragsdale S. W. Enzymology of the acetyl-CoA pathway of CO2 fixation. Crit Rev Biochem Mol Biol. 1991;26(3-4):261–300. doi: 10.3109/10409239109114070. [DOI] [PubMed] [Google Scholar]
  14. Ragsdale S. W., Ljungdahl L. G., DerVartanian D. V. 13C and 61Ni isotope substitutions confirm the presence of a nickel (III)-carbon species in acetogenic CO dehydrogenases. Biochem Biophys Res Commun. 1983 Sep 15;115(2):658–665. doi: 10.1016/s0006-291x(83)80195-8. [DOI] [PubMed] [Google Scholar]
  15. Ragsdale S. W., Ljungdahl L. G., DerVartanian D. V. Isolation of carbon monoxide dehydrogenase from Acetobacterium woodii and comparison of its properties with those of the Clostridium thermoaceticum enzyme. J Bacteriol. 1983 Sep;155(3):1224–1237. doi: 10.1128/jb.155.3.1224-1237.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ragsdale S. W., Wood H. G., Antholine W. E. Evidence that an iron-nickel-carbon complex is formed by reaction of CO with the CO dehydrogenase from Clostridium thermoaceticum. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6811–6814. doi: 10.1073/pnas.82.20.6811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Stephens P. J., McKenna M. C., Ensign S. A., Bonam D., Ludden P. W. Identification of a Ni- and Fe-containing cluster in Rhodospirillum rubrum carbon monoxide dehydrogenase. J Biol Chem. 1989 Oct 5;264(28):16347–16350. [PubMed] [Google Scholar]
  18. Terlesky K. C., Barber M. J., Aceti D. J., Ferry J. G. EPR properties of the Ni-Fe-C center in an enzyme complex with carbon monoxide dehydrogenase activity from acetate-grown Methanosarcina thermophila. Evidence that acetyl-CoA is a physiological substrate. J Biol Chem. 1987 Nov 15;262(32):15392–15395. [PubMed] [Google Scholar]
  19. Terlesky K. C., Nelson M. J., Ferry J. G. Isolation of an enzyme complex with carbon monoxide dehydrogenase activity containing corrinoid and nickel from acetate-grown Methanosarcina thermophila. J Bacteriol. 1986 Dec;168(3):1053–1058. doi: 10.1128/jb.168.3.1053-1058.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Wood H. G., Ragsdale S. W., Pezacka E. A new pathway of autotrophic growth utilizing carbon monoxide or carbon dioxide and hydrogen. Biochem Int. 1986 Mar;12(3):421–440. [PubMed] [Google Scholar]

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