Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open α subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase (original) (raw)
References
Huber, C. & Wachtershauser, G. Activated acetic acid by carbon fixation on (Fe, Ni)S under primordial conditions. Science276, 245–247 (1997). ArticleCAS Google Scholar
Wood, H.G. & Ljungdahl, L.G Autotrophic character of acetogenic bacteria. in Variation in Autotrophic Life (eds. Shively, J.M. & Barton, L.L.) 201–250 (Academic Press, New York; 1991). Google Scholar
Dobbek, H., Svetlitchnyi, V., Gremer, L., Huber, R. & Meyer, O. Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science293, 1281–1285 (2001). ArticleCAS Google Scholar
Drennan, C.L., Heo, J., Sintchak, M.D., Schreiter, E. & Ludden, P.W. Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. Proc. Natl. Acad. Sci. USA98, 11973–11978 (2001). ArticleCAS Google Scholar
Lindahl, P.A., Munck, E. & Ragsdale, S.W. CO dehydrogenase from Clostridium thermoaceticum. EPR and electrochemical studies in CO2 and argon atmospheres. J. Biol. Chem.265, 3873–3879 (1990). CASPubMed Google Scholar
Maynard, E.L. & Lindahl, P.A. Evidence of a molecular tunnel connecting the active sites for CO2 reduction and acetyl-CoA synthesis in acetyl-CoA synthase from Clostridium thermoaceticum. J. Am. Chem. Soc.121, 9221–9222 (1999). ArticleCAS Google Scholar
Seravalli, J. & Ragsdale, S.W. Channeling of carbon monoxide during anaerobic carbon dioxide fixation. Biochemistry39, 1274–1277 (2000). ArticleCAS Google Scholar
Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W. & Drennan, C.L. A Ni-Fe-Cu center in a bifuctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science298, 567–572 (2002). ArticleCAS Google Scholar
Lu, W.P., Harder, S.R. & Ragsdale, S.W. Controlled potential enzymology of methyl transfer reactions involved in acetyl-CoA synthesis by CO dehydrogenase and the corrinoid/iron-sulfur protein from Clostridium thermoaceticum. J. Biol. Chem.265, 3124–3133 (1990). CASPubMed Google Scholar
Barondeau, D.P. & Lindahl, P.A. Methylation of carbon monoxide dehydrogenase from Clostridium thermoaceticum and the mechanism of acetyl-CoA synthesis. J. Am. Chem. Soc.119, 3959–3970 (1997). ArticleCAS Google Scholar
Ragsdale, S.W. & Wood, H.G. Acetate biosynthesis by acetogenic bacteria. Evidence that carbon monoxide dehydrogenase is the condensing enzyme that catalyzes the final steps of the synthesis. J. Biol. Chem.260, 3970–3977 (1985). CASPubMed Google Scholar
Tucci, G.C. & Holm, R.H. Nickel-mediated formation of thio esters from bound methyl, thiols, and carbon monoxide: a possible reaction pathway of acetyl-coenzyme A synthase activity in nickel-containing carbon monoxide dehydrogenases. J. Am. Chem. Soc.117, 6489–6496 (1995). ArticleCAS Google Scholar
Montet, Y. et al. Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics. Nat. Struct. Biol.4, 523–526 (1997). ArticleCAS Google Scholar
Shin, W. & Lindahl, P.A. Function and CO binding properties of the NiFe complex in carbon monoxide dehydrogenase from Clostridium thermoaceticum. Biochemistry31, 12870–12875 (1992). ArticleCAS Google Scholar
Tan, X.S., Sewell, C., Yang, Q. & Lindahl, P.A. Reduction and methyl transfer kinetics of the α subunit from acetyl-coenzyme A synthase. J. Am. Chem. Soc.125, 318–319 (2003). ArticleCAS Google Scholar
Tan, X.S., Sewell, C. & Lindahl, P.A. Stopped-flow kinetics of methyl group transfer between the corrinoid-iron-sulfur protein and acetyl-coenzyme A synthase from Clostridium thermoaceticum. J. Am. Chem. Soc.124, 6277–6284 (2002). ArticleCAS Google Scholar
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. Commun115, 658–665 (1983). ArticleCAS Google Scholar
Ragsdale, S.W., Wood, H.G. & Antholine, W.E. Evidence that an iron-nickel-carbon complex is formed by reaction of carbon monoxide with the carbon monoxide dehydrogenase from Clostridium thermoaceticum. Proc. Natl. Acad. Sci. USA82, 6811–6814 (1985). ArticleCAS Google Scholar
Xia, J. & Lindahl, P.A. Assembly of an exchange-coupled [Ni:′Fe4S4] cluster in the α metallosubunit of CO dehydrogenase from Clostridium thermoaceticum with spectroscopic properties and CO-binding ability mimicking those of the acetyl-CoA synthase active site. J. Am. Chem. Soc.118, 483–484 (1996). ArticleCAS Google Scholar
Russell, W.K., Stålhandske, C.M.V., Xia, J., Scott, R.A. & Lindahl, P.A. Spectroscopic, redox and structural characterization of the Ni-labile and nonlabile forms of the acetyl-CoA synthase active site of CO dehydrogenase. J. Am. Chem. Soc.120, 7502–7510 (1998). ArticleCAS Google Scholar
Shin, W., Anderson, M.E. & Lindahl, P.A. Heterogeneous nickel environments in carbon monoxide dehydrogenase from Clostridium thermoaceticum. J. Am. Chem. Soc.115, 5522–5526 (1993). ArticleCAS Google Scholar
Shin, W. & Lindahl, P.A. Low spin quantitation of NiFeC EPR signal from carbon monoxide dehydrogenase is not due to damage incurred during protein purification. Biochim. Biophys. Acta1161, 317–322 (1993). ArticleCAS Google Scholar
Lindahl, P.A., Ragsdale, S.W. & Münck, E. Mössbauer study of CO dehydrogenase from Clostridium thermoaceticum. J. Biol. Chem.265, 3880–3888 (1990). CASPubMed Google Scholar
Wilson, B.E. & Lindahl, P.A. Equilibrium dialysis study and mechanistic implications of coenzyme A binding to acetyl-CoA synthase/carbon monoxide dehydrogenase from Clostridium thermoaceticum. J. Biol. Inorg. Chem.4, 742–748 (1999). ArticleCAS Google Scholar
Musie, G., Farmer, P.J., Tuntulani, T., Reibenspies, J.H. & Darensbourg, M.Y. Influence of sulfur metalation on the accessibility of the NiII/I couple in [N, _N_′-Bis(2-mercaptoethyl)-1,5-diazacyclootanato]nickel(II): insight into the redox properties of [NiFe]-hydrogenase. Inorg. Chem.35, 2176–2183 (1996). ArticleCAS Google Scholar
Lai, C.-H., Reibenspies, J.H. & Darensbourg, M.Y. Thiolate bridged nickel-iron complexes containing both iron(0) and iron(II) carbonyls. Angew. Chem. Int. Ed. Engl.35, 2390–2393 (1996). ArticleCAS Google Scholar
Bouwman, E., Henderson, R.K., Spek, A.L. & Reedijk, J. Spontaneous assembly of a novel tetranuclear Ni-Fe complex by complete reshuffling of ligands and oxidation states. Eur. J. Inorg. Chem.1999, 217–219 (1999). Article Google Scholar
Tolman, C.A. Electron donor-acceptor properties of phosphorus ligands. Substituent additivity. J. Am. Chem. Soc.92, 2953–2956 (1970). ArticleCAS Google Scholar
Shultz, C.S., DeSimone, J.M. & Brookhart, M. Four- and five-coordinate CO insertion mechanisms in d8-nickel(II) complexes. J. Am. Chem. Soc.123, 9172–9173 (2001). ArticleCAS Google Scholar
Tolman, C.A., Seidel, W.C. & Gosser, L.W. Formation of three-coordinate nickel(0) complexes by phosphorus ligand dissociation from NiL4 . J. Am. Chem. Soc.96, 53–60 (1973). Article Google Scholar
Hsiao, Y.-M., Chojnacki, S.S., Hinton, P., Reibenspies, J.H. & Darensbourg, M.Y. Organometallic chemistry of sulfur/phosphorus donor ligand complexes of nickel(II) and nickel(0). Organometallics12, 870–875 (1993). ArticleCAS Google Scholar
Cotton, F.A. & Wilkinson, G. The chemistry of the transition elements. in Advanced Inorganic Chemistry 5th edn. 741–754 (Wiley, New York; 1997). Google Scholar
Volbeda, A. et al. Structure of the (NiFe) hydrogenase active site: evidence for biologically uncommon Fe ligands. J. Am. Chem. Soc.118, 12989–12996 (1996). ArticleCAS Google Scholar
Fan, C., Gorst, C.M., Ragsdale, S.W. & Hoffman, B.M. Characterization of the nickel-iron-carbon complex formed by reaction of carbon monoxide with the carbon monoxide dehydrogenase from Clostridium thermoaceticum by Q-band ENDOR. Biochemistry30, 431–435 (1991). ArticleCAS Google Scholar
Collman, J.P., Hegedus, L.S., Norton, J.R. & Finke, R.G. Intramolecular insertion reactions. in Principles and Applications of Organotransition Metal Chemistry 355–399 (University Science Books, Mill Valley; 1987). Google Scholar
Gencic, S. & Grahame, D.A. Nickel in subunit β of the acetyl-CoA decarbonylase/synthetase multienzyme complex in methanogens. J. Biol. Chem.278, 6101–6110 (2003). ArticleCAS Google Scholar
Lundie, L.L. Jr. & Drake, H.L. Development of a minimally defined medium for the acetogen Clostridium thermoaceticum. J. Bacteriol.159, 700–703 (1984). CASPubMedPubMed Central Google Scholar
Vernède, X. & Fontecilla-Camps, J.C. A method to stabilize reduced and/or gas-treated protein crystals by flash-cooling under a controlled atmosphere. J. Appl. Crystallogr.32, 505–509 (1999). Article Google Scholar
Kabsch, W. Integration, scaling, space-group assignment and post refinement. in International Tables for Crystallography, Volume F, Crystallography of Biological Macromolecules (eds. Rossmann, M.G. & Arnold, E.) Ch. 11.3 (Kluwer Academic Publishers, Dordrecht; 2001). Google Scholar
Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50, 157–163 (1994). Article Google Scholar
Terwilliger, T.C. & Berendzen, J. Automated structure solution for MIR and MAD. Acta Crystallogr. D55, 849–861 (1999). ArticleCAS Google Scholar
Read, R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149 (1986). Article Google Scholar
Perrakis, A., Morris, R.J. & Lamzin, V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol.6, 458–463 (1999). ArticleCAS Google Scholar
Roussel, A. & Cambillau, C. Turbo-Frodo (Silicon Graphics, Mountain View; 1989).
Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likehood method. Acta Crystallogr. D53, 240–255 (1997). ArticleCAS Google Scholar
Winn, M.D., Isupov, M.N. & Murshudov, G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D57, 122–133 (2001). ArticleCAS Google Scholar
Volbeda, A. Spéléologie des hydrogenases à nickel et à fer. Les écoles physique et chimie du vivant1, 47–52 (1999). Google Scholar
Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr.24, 946–950 (1991). Article Google Scholar
Lawrence, M.C. & Bourke, P. A program for generating electron density isosurfaces from Fourier syntheses in protein crystallography. J. Appl. Crystallogr.33, 990–991 (2000). ArticleCAS Google Scholar