The extended reductive acetyl-CoA pathway: ATPases in metal cluster maturation and reductive activation

References

Ando, N., Kung, Y., Can, M., Bender, G., Ragsdale, S.W., and Drennan, C.L. (2012). Transient B12-dependent methyltransferase complex revealed by small-angle X-ray scattering. J. Am. Chem. Soc. 134, 17945–17954.10.1021/ja3055782Search in Google Scholar

Appel, A.M., Bercaw, J.E., Bocarsly, A.B., Dobbek, H., Dubois, D.L., Dupuis, M., Ferry, J.G., Fujita, E., Hille, R., Kenis, P.J., et al. (2013). Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO fixation. Chem. Rev. 113, 6621–6658.10.1021/cr300463ySearch in Google Scholar

Berg, I.A., Kockelkorn, D., Ramos-Vera, W.H., Say, R.F., Zarzycki, J., Hugler, M., Alber, B.E., and Fuchs, G. (2010). Autotrophic carbon fixation in archaea. Nat. Rev. Microbiol. 8, 447–460.10.1038/nrmicro2365Search in Google Scholar

Blokesch, M., Paschos, A., Theodoratou, E., Bauer, A., Hube, M., Huth, S., and Bock, A. (2002). Metal insertion into NiFe-hydrogenases. Biochem. Soc. Trans. 30, 674–680.10.1042/bst0300674Search in Google Scholar

Boer, J.L., Mulrooney, S.B., and Hausinger, R.P. (2014). Nickel-dependent metalloenzymes. Arch. Biochem. Biophys. 544, 142–152.10.1016/j.abb.2013.09.002Search in Google Scholar

Chan, J.M., Ryle, M.J., and Seefeldt, L.C. (1999). Evidence that MgATP accelerates primary electron transfer in a Clostridium pasteurianum Fe protein-Azotobacter vinelandii MoFe protein nitrogenase tight complex. J. Biol. Chem. 274, 17593–17598.10.1074/jbc.274.25.17593Search in Google Scholar

Cordell, S.C. and Lowe, J. (2001). Crystal structure of the bacterial cell division regulator MinD. FEBS Lett. 492, 160–165.10.1016/S0014-5793(01)02216-5Search in Google Scholar

Craft, J.L., Ludden, P.W., and Brunold, T.C. (2002). Spectroscopic studies of nickel-deficient carbon monoxide dehydrogenase from Rhodospirillum rubrum: nature of the iron-sulfur clusters. Biochemistry 41, 1681–1688.10.1021/bi011586kSearch in Google Scholar PubMed

Darnault, C., Volbeda, A., Kim, E.J., Legrand, P., Vernede, X., Lindahl, P.A., and Fontecilla-Camps, J.C. (2003). Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat. Struct. Biol. 10, 271–279.10.1038/nsb912Search in Google Scholar PubMed

Diekert, G.B. and Thauer, R.K. (1978). Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum. J. Bacteriol. 136, 597–606.10.1128/jb.136.2.597-606.1978Search in Google Scholar PubMed PubMed Central

Dobbek, H. and Huber, R. (2001). CO dehydrogenase. In: Handbook of Metalloproteins. Messerschmidt, A., Huber, R., Wieghardt, K., and Poulos, T., eds. (New York: John Wiley & Sons), pp. 1136–1147.Search in Google Scholar

Dobbek, H., Svetlitchnyi, V., Gremer, L., Huber, R., and Meyer, O. (2001). Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science 293, 1281–1285.10.1126/science.1061500Search in Google Scholar

Dobbek, H., Gremer, L., Kiefersauer, R., Huber, R., and Meyer, O. (2002). Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1 Å resolution. Proc. Natl. Acad. Sci. USA 99, 15971–15976.10.1073/pnas.212640899Search in Google Scholar

Dobbek, H., Svetlitchnyi, V., Liss, J., and Meyer, O. (2004). Carbon monoxide induced decomposition of the active site [Ni-4Fe-5S] cluster of CO dehydrogenase. J. Am. Chem. Soc. 126, 5382–5387.10.1021/ja037776vSearch in Google Scholar

Doukov, T.I., Iverson, T.M., Seravalli, J., Ragsdale, S.W., and Drennan, C.L. (2002). A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science 298, 567–572.10.1126/science.1075843Search in Google Scholar

Drake, H.L., Hu, S.I., and Wood, H.G. (1980). Purification of carbon monoxide dehydrogenase, a nickel enzyme from Clostridium thermoaceticum. J. Biol. Chem. 255, 7174–7180.10.1016/S0021-9258(20)79682-1Search in Google Scholar

Drapal, N. and Bock, A. (1998). Interaction of the hydrogenase accessory protein HypC with HycE, the large subunit of Escherichia coli hydrogenase 3 during enzyme maturation. Biochemistry 37, 2941–2948.10.1021/bi9720078Search in Google Scholar PubMed

Drennan, C.L., Heo, J.Y., Sintchak, M.D., Schreiter, E., and Ludden, P.W. (2001). Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. Proc. Natl. Acad. Sci. USA 98, 11973–11978.10.1073/pnas.211429998Search in Google Scholar PubMed PubMed Central

Drennan, C.L., Doukov, T.I., and Ragsdale, S.W. (2004). The metalloclusters of carbon monoxide dehydrogenase/acetyl-CoA synthase: a story in pictures. J. Biol. Inorg. Chem. 9, 511–515.10.1007/s00775-004-0563-ySearch in Google Scholar PubMed

Farrugia, M.A., Macomber, L., and Hausinger, R.P. (2013). Biosynthesis of the urease metallocenter. J. Biol. Chem. 288, 13178–13185.10.1074/jbc.R112.446526Search in Google Scholar PubMed PubMed Central

Fay, A.W., Blank, M.A., Yoshizawa, J.M., Lee, C.C., Wiig, J.A., Hu, Y., Hodgson, K.O., Hedman, B., and Ribbe, M.W. (2010). Formation of a homocitrate-free iron-molybdenum cluster on NifEN: implications for the role of homocitrate in nitrogenase assembly. Dalton Trans. 39, 3124–3130.10.1039/c000264jSearch in Google Scholar PubMed PubMed Central

Feng, J. and Lindahl, P.A. (2004). Effect of sodium sulfide on Ni-containing carbon monoxide dehydrogenases. J. Am. Chem. Soc. 126, 9094–9100.10.1021/ja048811gSearch in Google Scholar PubMed

Ferguson, T., Soares, J.A., Lienard, T., Gottschalk, G., and Krzycki, J.A. (2009). RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. J. Biol. Chem. 284, 2285–2295.10.1074/jbc.M807392200Search in Google Scholar PubMed PubMed Central

Flaherty, K.M., McKay, D.B., Kabsch, W., and Holmes, K.C. (1991). Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc. Natl. Acad. Sci. USA 88, 5041–5045.10.1073/pnas.88.11.5041Search in Google Scholar PubMed PubMed Central

Fontecilla-Camps, J.C., Amara, P., Cavazza, C., Nicolet, Y., and Volbeda, A. (2009). Structure-function relationships of anaerobic gas-processing metalloenzymes. Nature 460, 814–822.10.1038/nature08299Search in Google Scholar PubMed

Forzi, L. and Sawers, R.G. (2007). Maturation of [NiFe]-hydrogenases in Escherichia coli. Biometals 20, 565–578.10.1007/s10534-006-9048-5Search in Google Scholar PubMed

Fuchs, G. (2011). Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658.10.1146/annurev-micro-090110-102801Search in Google Scholar PubMed

Gencic, S., Duin, E.C., and Grahame, D.A. (2010). Tight coupling of partial reactions in the acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex from Methanosarcina thermophila: acetyl C-C bond fragmentation at the a cluster promoted by protein conformational changes. J. Biol. Chem. 285, 15450–15463.10.1074/jbc.M109.080994Search in Google Scholar PubMed PubMed Central

Georgiadis, M.M., Komiya, H., Chakrabarti, P., Woo, D., Kornuc, J.J., and Rees, D.C. (1992). Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. Science 257, 1653–1659.10.1126/science.1529353Search in Google Scholar PubMed

Goetzl, S., Jeoung, J.H., Hennig, S.E., and Dobbek, H. (2011). Structural basis for electron and methyl group transfer in a methyltransferase system operating in the reductive acetyl-CoA pathway. J. Mol. Biol. 411, 96–109.10.1016/j.jmb.2011.05.025Search in Google Scholar PubMed

Gong, W., Hao, B., Ferguson, D.J., Jr., Tallant, T., Krzycki, J.A., and Chan, M.K. (2008). Structure of the alpha2epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex. Proc. Natl. Acad. Sci. USA 105, 9558–9563.10.1073/pnas.0800415105Search in Google Scholar PubMed PubMed Central

Grahame, D.A. (1991). Catalysis of acetyl-CoA cleavage and tetrahydrosarcinapterin methylation by a carbon monoxide dehydrogenase-corrinoid enzyme complex. J. Biol. Chem. 266, 22227–22233.10.1016/S0021-9258(18)54558-0Search in Google Scholar

Grahame, D.A. and Stadtman, T.C. (1987). Carbon monoxide dehydrogenase from Methanosarcina barkeri. Disaggregation, purification, and physicochemical properties of the enzyme. J. Biol. Chem. 262, 3706–3712.10.1016/S0021-9258(18)61412-7Search in Google Scholar

Ha, S.W., Korbas, M., Klepsch, M., Meyer-Klaucke, W., Meyer, O., and Svetlitchnyi, V. (2007). Interaction of potassium cyanide with the [Ni-4Fe-5S] active site cluster of CO dehydrogenase from Carboxydothermus hydrogenoformans. J. Biol. Chem. 282, 10639–10646.10.1074/jbc.M610641200Search in Google Scholar PubMed

Harder, S.R., Lu, W.P., Feinberg, B.A., and Ragsdale, S.W. (1989). Spectroelectrochemical studies of the corrinoid/iron-sulfur protein involved in acetyl coenzyme A synthesis by Clostridium thermoaceticum. Biochemistry 28, 9080–9087.10.1021/bi00449a019Search in Google Scholar PubMed

Hayashi, I., Oyama, T., and Morikawa, K. (2001). Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus. EMBO J. 20, 1819–1828.10.1093/emboj/20.8.1819Search in Google Scholar PubMed PubMed Central

Hennig, S.E., Jeoung, J.H., Goetzl, S., and Dobbek, H. (2012). Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein. Proc. Natl. Acad. Sci. USA 109, 5235–5240.10.1073/pnas.1117126109Search in Google Scholar PubMed PubMed Central

Herrmann, G., Jayamani, E., Mai, G., and Buckel, W. (2008). Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J. Bacteriol. 190, 784–791.10.1128/JB.01422-07Search in Google Scholar PubMed PubMed Central

Hu, Y. and Ribbe, M.W. (2011a). Biosynthesis of nitrogenase Femoco. Coord. Chem. Rev. 255, 1218–1224.10.1016/j.ccr.2010.11.018Search in Google Scholar PubMed PubMed Central

Hu, Y. and Ribbe, M.W. (2011b). Biosynthesis of the metalloclusters of molybdenum nitrogenase. Microbiol. Mol. Biol. Rev. 75, 664–677.10.1128/MMBR.05008-11Search in Google Scholar PubMed PubMed Central

Hu, Y. and Ribbe, M.W. (2013a). Biosynthesis of the iron-molybdenum cofactor of nitrogenase. J. Biol. Chem. 288, 13173–13177.10.1074/jbc.R113.454041Search in Google Scholar PubMed PubMed Central

Hu, Y. and Ribbe, M.W. (2013b). Nitrogenase assembly. Biochim. Biophys. Acta 1827, 1112–1122.10.1016/j.bbabio.2012.12.001Search in Google Scholar PubMed PubMed Central

Hu, Y.L., Corbett, M.C., Fay, A.W., Webber, J.A., Hodgson, K.O., Hedman, B., and Ribbe, M.W. (2006). FeMo cofactor maturation on NifEN. Proc. Natl. Acad. Sci. USA 103, 17119–17124.10.1073/pnas.0602647103Search in Google Scholar PubMed PubMed Central

Hu, Y., Fay, A.W., Lee, C.C., Wiig, J.A., and Ribbe, M.W. (2010). Dual functions of NifEN: insights into the evolution and mechanism of nitrogenase. Dalton Trans. 39, 2964–2971.10.1039/b922555bSearch in Google Scholar PubMed PubMed Central

Hurley, J.H. (1996). The sugar kinase/heat shock protein 70/actin superfamily: implications of conserved structure for mechanism. Annu. Rev. Biophys. Biomol. Struct. 25, 137–162.10.1146/annurev.bb.25.060196.001033Search in Google Scholar PubMed

Jeon, W.B., Cheng, J.J., and Ludden, P.W. (2001). Purification and characterization of membrane-associated CooC protein and its functional role in the insertion of nickel into carbon monoxide dehydrogenase from Rhodospirillum rubrum. J. Biol. Chem. 276, 38602–38609.10.1074/jbc.M104945200Search in Google Scholar PubMed

Jeoung, J.H. and Dobbek, H. (2007a). Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase. Science 318, 1461–1464.10.1126/science.1148481Search in Google Scholar PubMed

Jeoung, J.H. and Dobbek, H. (2007b). Ni-containing carbon monoxide dehydrogenase. In: Handbook of Metalloproteins. Messerschmidt, A., ed. (New York: John Wiley & Sons).10.1002/0470028637.met213Search in Google Scholar

Jeoung, J.H. and Dobbek, H. (2009). Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase. J. Am. Chem. Soc. 131, 9922–9923.10.1021/ja9046476Search in Google Scholar PubMed

Jeoung, J.H., Giese, T., Grünwald, M., and Dobbek, H. (2009). CooC1 from carboxydothermus hydrogenoformans is a nickel-binding ATPase. Biochemistry 48, 11505–11513.10.1021/bi901443zSearch in Google Scholar PubMed

Jeoung, J.H., Giese, T., Grunwald, M., and Dobbek, H. (2010). Crystal structure of the ATP-dependent maturation factor of Ni,Fe-containing carbon monoxide dehydrogenases. J. Mol. Biol. 396, 1165–1179.10.1016/j.jmb.2009.12.062Search in Google Scholar PubMed

Kabsch, W. and Holmes, K.C. (1995). The actin fold. FASEB J. 9, 167–174.10.1096/fasebj.9.2.7781919Search in Google Scholar PubMed

Kaluarachchi, H., Chan Chung, K.C., and Zamble, D.B. (2010). Microbial nickel proteins. Nat. Prod. Rep. 27, 681–694.10.1039/b906688hSearch in Google Scholar PubMed

Kaster, A.K., Moll, J., Parey, K., and Thauer, R.K. (2011). Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA 108, 2981–2986.10.1073/pnas.1016761108Search in Google Scholar PubMed PubMed Central

Kerby, R.L., Ludden, P.W., and Roberts, G.P. (1997). In vivo nickel insertion into the carbon monoxide dehydrogenase of Rhodospirillum rubrum: Molecular and physiological characterization of cooCTJ. J. Bacteriol. 179, 2259–2266.10.1128/jb.179.7.2259-2266.1997Search in Google Scholar PubMed PubMed Central

Krzycki, J.A. and Zeikus, J.G. (1984). Characterization and purification of carbon monoxide dehydrogenase from Methanosarcina barkeri. J. Bacteriol. 158, 231–237.10.1128/jb.158.1.231-237.1984Search in Google Scholar PubMed PubMed Central

Kuchenreuther, J.M., Britt, R.D., and Swartz, J.R. (2012). New insights into [FeFe] hydrogenase activation and maturase function. PLoS One 7, e45850.10.1371/journal.pone.0045850Search in Google Scholar PubMed PubMed Central

Kung, Y., Doukov, T.I., Seravalli, J., Ragsdale, S.W., and Drennan, C.L. (2009). Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry 48, 7432–7440.10.1021/bi900574hSearch in Google Scholar PubMed PubMed Central

Kung, Y., Ando, N., Doukov, T.I., Blasiak, L.C., Bender, G., Seravalli, J., Ragsdale, S.W., and Drennan, C.L. (2012). Visualizing molecular juggling within a B12-dependent methyltransferase complex. Nature 484, 265–269.10.1038/nature10916Search in Google Scholar PubMed PubMed Central

Leach, M.R. and Zamble, D.B. (2007). Metallocenter assembly of the hydrogenase enzymes. Curr. Opin. Chem. Biol. 11, 159–165.10.1016/j.cbpa.2007.01.011Search in Google Scholar PubMed

Leipe, D.D., Wolf, Y.I., Koonin, E.V., and Aravind, L. (2002). Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317, 41–72.10.1006/jmbi.2001.5378Search in Google Scholar PubMed

Leonard, T.A., Butler, P.J., and Lowe, J. (2005). Bacterial chromosome segregation: structure and DNA binding of the Soj dimer-a conserved biological switch. EMBO J. 24, 270–282.10.1038/sj.emboj.7600530Search in Google Scholar

Li, Y. and Zamble, D.B. (2009). Nickel homeostasis and nickel regulation: an overview. Chem. Rev. 109, 4617–4643.10.1021/cr900010nSearch in Google Scholar

Li, F., Hinderberger, J., Seedorf, H., Zhang, J., Buckel, W., and Thauer, R.K. (2008). Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J. Bacteriol. 190, 843–850.10.1128/JB.01417-07Search in Google Scholar

Loke, H.K. and Lindahl, P.A. (2003). Identification and preliminary characterization of AcsF, a putative Ni-insertase used in the biosynthesis of acetyl-CoA synthase from Clostridium thermoaceticum. J. Inorg. Biochem. 93, 33–40.10.1016/S0162-0134(02)00457-9Search in Google Scholar

Lutkenhaus, J. (2007). Assembly dynamics of the bacterial MinCDE system and spatial regulation of the Z ring. Annu. Rev. Biochem. 76, 539–562.10.1146/annurev.biochem.75.103004.142652Search in Google Scholar

Lutkenhaus, J. and Sundaramoorthy, M. (2003). MinD and role of the deviant Walker A motif, dimerization and membrane binding in oscillation. Mol. Microbiol. 48, 295–303.10.1046/j.1365-2958.2003.03427.xSearch in Google Scholar

Marcus, R.A. and Sutin, N. (1985). Electron transfers in chemistry and biology. Biochim. Biophys. Acta 811, 265–322.10.1016/0304-4173(85)90014-XSearch in Google Scholar

Martin, W. and Russell, M.J. (2007). On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 362, 1887–1925.10.1098/rstb.2006.1881Search in Google Scholar PubMed PubMed Central

Mateja, A., Szlachcic, A., Downing, M.E., Dobosz, M., Mariappan, M., Hegde, R.S., and Keenan, R.J. (2009). The structural basis of tail-anchored membrane protein recognition by Get3. Nature 461, 361–366.10.1038/nature08319Search in Google Scholar PubMed PubMed Central

Matthews, R.G. (2001). Cobalamin-dependent methyltransferases. Acc. Chem. Res. 34, 681–689.10.1021/ar0000051Search in Google Scholar PubMed

Matthews, R.G., Koutmos, M., and Datta, S. (2008). Cobalamin-dependent and cobamide-dependent methyltransferases. Curr. Opin. Struct. Biol. 18, 658–666.10.1016/j.sbi.2008.11.005Search in Google Scholar

Meister, W., Hennig, S.E., Jeoung, J.H., Lendzian, F., Dobbek, H., and Hildebrandt, P. (2012). Complex formation with the activator RACo affects the corrinoid structure of CoFeSP. Biochemistry 51, 7040–7042.10.1021/bi300795nSearch in Google Scholar

Menon, S. and Ragsdale, S.W. (1998). Role of the [4Fe-4S] cluster in reductive activation of the cobalt center of the corrinoid iron-sulfur protein from Clostridium thermoaceticum during acetate biosynthesis. Biochemistry 37, 5689–5698.10.1021/bi9727996Search in Google Scholar

Menon, S. and Ragsdale, S.W. (1999). The role of an iron-sulfur cluster in an enzymatic methylation reaction. Methylation of CO dehydrogenase/acetyl-CoA synthase by the methylated corrinoid iron-sulfur protein. J. Biol. Chem. 274, 11513–11518.10.1074/jbc.274.17.11513Search in Google Scholar

Meyer, O., Gremer, L., Ferner, R., Ferner, M., Dobbek, H., Gnida, M., Meyer-Klaucke, W., and Huber, R. (2000). The role of Se, Mo and Fe in the structure and function of carbon monoxide dehydrogenase. Biol. Chem. 381, 865–876.10.1515/BC.2000.108Search in Google Scholar

Moncrief, M.B. and Hausinger, R.P. (1997). Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. J. Bacteriol. 179, 4081–4086.10.1128/jb.179.13.4081-4086.1997Search in Google Scholar

Mulrooney, S.B. and Hausinger, R.P. (2003). Nickel uptake and utilization by microorganisms. Fems. Microbiol. Rev. 27, 239–261.10.1016/S0168-6445(03)00042-1Search in Google Scholar

Nguyen, H.D., Studenik, S., and Diekert, G. (2013). Corrinoid activation by a RACE protein: studies on the interaction of the proteins involved. FEMS Microbiol. Lett. 345, 31–38.10.1111/1574-6968.12178Search in Google Scholar PubMed

Nicolet, Y. and Fontecilla-Camps, J.C. (2012). Structure-function relationships in [FeFe]-hydrogenase active site maturation. J. Biol. Chem. 287, 13532–13540.10.1074/jbc.R111.310797Search in Google Scholar PubMed PubMed Central

Oelgeschläger, E. and Rother, M. (2008). Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Arch. Microbiol. 190, 257–269.10.1007/s00203-008-0382-6Search in Google Scholar PubMed

Page, C.C., Moser, C.C., Chen, X., and Dutton, P.L. (1999). Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature 402, 47–52.10.1038/46972Search in Google Scholar PubMed

Ragsdale, S.W. (2004). Life with carbon monoxide. Crit. Rev. Biochem. Mol. Biol. 39, 165–195.10.1080/10409230490496577Search in Google Scholar PubMed

Ragsdale, S.W. (2006). Metals and their scaffolds to promote difficult enzymatic reactions. Chem. Rev. 106, 3317–3337.10.1021/cr0503153Search in Google Scholar PubMed

Ragsdale, S.W. (2007). Nickel and the carbon cycle. J. Inorg. Biochem. 101, 1657–1666.10.1016/j.jinorgbio.2007.07.014Search in Google Scholar PubMed PubMed Central

Ragsdale, S.W. (2008). Enzymology of the wood-Ljungdahl pathway of acetogenesis. Ann. NY. Acad. Sci. 1125, 129–136.10.1196/annals.1419.015Search in Google Scholar PubMed PubMed Central

Ragsdale, S.W. (2009). Nickel-based Enzyme Systems. J. Biol. Chem. 284, 18571–18575.10.1074/jbc.R900020200Search in Google Scholar PubMed PubMed Central

Ragsdale, S.W. and Pierce, E. (2008). Acetogenesis and the Wood-Ljungdahl pathway of CO₂ fixation. Biochim. Biophys. Acta 1784, 1873–1898.10.1016/j.bbapap.2008.08.012Search in Google Scholar PubMed PubMed Central

Ragsdale, S.W., Wood, H.G., and Antholine, W.E. (1985). Evidence that an iron-nickel-carbon complex is formed by reaction of CO with the CO dehydrogenase from Clostridium thermoaceticum. Proc. Natl. Acad. Sci. USA 82, 6811–6814.10.1073/pnas.82.20.6811Search in Google Scholar PubMed PubMed Central

Rees, D.C. and Howard, J.B. (1999). Structural bioenergetics and energy transduction mechanisms. J. Mol. Biol. 293, 343–350.10.1006/jmbi.1999.3005Search in Google Scholar PubMed

Robb, F.T., Gonzalez, J. M., Sokolova, T.G., Techtmann, S.M., Chernyh, N., Lebedinski, A., Tallon, L.J., Jones, K., Wu, M., and Eisen, J.A. (2005). Primary energy metabolism in geothermal environments: the role of carbon monoxide. In: Geothermal Biology and Geochemistry in Yellowstone Nation Park, W.P. Inskeep and T.R. McDermontt, eds. (Bozeman, MT: Montana State University Thermal Biology Institute), pp. 163–170.Search in Google Scholar

Roberts, G.P., Youn, H., and Kerby, R.L. (2004). CO-sensing mechanisms. Microbiol. Molbiol. Rev. 68, 453–473.10.1128/MMBR.68.3.453-473.2004Search in Google Scholar PubMed PubMed Central

Roberts, G.P., Kerby, R.L., Youn, H., and Conrad, M. (2005). CooA, a paradigm for gas sensing regulatory proteins. J. Inorg. Biochem. 99, 280–292.10.1016/j.jinorgbio.2004.10.032Search in Google Scholar

Russell, M.J. and Martin, W. (2004). The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci. 29, 358–363.10.1016/j.tibs.2004.05.007Search in Google Scholar

Sakai, N., Yao, M., Itou, H., Watanabe, N., Yumoto, F., Tanokura, M., and Tanaka, I. (2001). The three-dimensional structure of septum site- determining protein MinD from Pyrococcus horikoshii OT3 in complex with Mg-ADP. Structure 9, 817–826.10.1016/S0969-2126(01)00638-4Search in Google Scholar

Schilhabel, A., Studenik, S., Vodisch, M., Kreher, S., Schlott, B., Pierik, A.J., and Diekert, G. (2009). The ether-cleaving methyltransferase system of the strict anaerobe Acetobacterium dehalogenans: analysis and expression of the encoding genes. J. Bacteriol. 191, 588–599.10.1128/JB.01104-08Search in Google Scholar PubMed PubMed Central

Schindelin, N., Kisker, C., Sehlessman, J.L., Howard, J.B., and Rees, D.C. (1997). Structure of ADP^. AIF^4--stabilized nitrogenase complex and its implications for signal transduction. Nature 387, 370–376.10.1038/387370a0Search in Google Scholar PubMed

Seravalli, J. and Ragsdale, S.W. (2008). C-13 NMR characterization of an exchange reaction between CO and CO₂ catalyzed by carbon monoxide dehydrogenase. Biochemistry 47, 6770–6781.10.1021/bi8004522Search in Google Scholar PubMed PubMed Central

Shelver, D., Kerby, R.L., He, Y., and Roberts, G.P. (1995). Carbon monoxide-induced activation of gene expression in Rhodospirillum rubrum requires the product of cooA, a member of the cyclic AMP receptor protein family of transcriptional regulators. J. Bacteriol. 177, 2157–2163.10.1128/jb.177.8.2157-2163.1995Search in Google Scholar PubMed PubMed Central

Siebert, A., Schubert, T., Engelmann, T., Studenik, S., and Diekert, G. (2005). Veratrol-O-demethylase of Acetobacterium dehalogenans: ATP-dependent reduction of the corrinoid protein. Arch. Microbiol. 183, 378–384.10.1007/s00203-005-0001-8Search in Google Scholar PubMed

Svetlitchnaia, T., Svetlitchnyi, V., Meyer, O., and Dobbek, H. (2006). Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis. Proc. Natl. Acad. Sci. USA 103, 14331–14336.10.1073/pnas.0601420103Search in Google Scholar PubMed PubMed Central

Svetlitchnyi, V., Peschel, C., Acker, G., and Meyer, O. (2001). Two membrane-associated NiFeS-carbon monoxide dehydrogenases from the anaerobic carbon monoxide utilizing eubacterium Carboxydothermus hydrogenoformans. J. Bacteriol. 183, 5134–5144.10.1128/JB.183.17.5134-5144.2001Search in Google Scholar PubMed PubMed Central

Svetlitchnyi, V., Dobbek, H., Meyer-Klaucke, W., Meins, T., Thiele, B., Romer, P., Huber, R., and Meyer, O. (2004). A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans. Proc. Natl. Acad. Sci. USA 101, 446–451.10.1073/pnas.0304262101Search in Google Scholar PubMed PubMed Central

Techtmann, S.M., Colman, A.S., and Robb, F.T. (2009). ‘That which does not kill us only makes us stronger’: the role of carbon monoxide in thermophilic microbial consortia. Environ. Microbiol. 11, 1027–1037.10.1111/j.1462-2920.2009.01865.xSearch in Google Scholar PubMed

Techtmann, S.M., Colman, A.S., Murphy, M.B., Schackwitz, W.S., Goodwin, L.A., and Robb, F.T. (2011). Regulation of multiple carbon monoxide consumption pathways in anaerobic bacteria. Front. Microbiol. 2, 147.10.3389/fmicb.2011.00147Search in Google Scholar PubMed PubMed Central

Volbeda, A. and Fontecilla-Camps, J.C. (2005). Structural bases for the catalytic mechanism of Ni-containing carbon monoxide dehydrogenases. Dalton Trans. 2, 3443–3450.10.1039/b508403bSearch in Google Scholar PubMed

Volbeda, A. and Fontecilla-Camps, J.C. (2006). Catalytic nickel–iron-sulfur clusters: from minerals to enzymes. Top. Organomet. Chem. 17, 57–82.10.1007/3418_003Search in Google Scholar

Wang, S., Huang, H., Moll, J., and Thauer, R.K. (2010). NADP⁺ reduction with reduced ferredoxin and NADP⁺ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. J. Bacteriol. 192, 5115–5123.10.1128/JB.00612-10Search in Google Scholar PubMed PubMed Central

Wang, V.C., Can, M., Pierce, E., Ragsdale, S.W., and Armstrong, F.A. (2013a). A unified electrocatalytic description of the action of inhibitors of nickel carbon monoxide dehydrogenase. J. Am. Chem. Soc. 135, 2198–2206.10.1021/ja308493kSearch in Google Scholar PubMed PubMed Central

Wang, V.C., Ragsdale, S.W., and Armstrong, F.A. (2013b). Investigations of two bidirectional carbon monoxide dehydrogenases from Carboxydothermus hydrogenoformans by protein film electrochemistry. Chembiochem 14, 1845–1851.10.1002/cbic.201300270Search in Google Scholar PubMed PubMed Central

Watt, R.K. and Ludden, P.W. (1998). The identification, purification, and characterization of CooJ. A nickel-binding protein that is co-regulated with the Ni-containing CO dehydrogenase from Rhodospirillum rubrum. J. Biol. Chem. 273, 10019–10025.10.1074/jbc.273.16.10019Search in Google Scholar PubMed

Watt, R.K. and Ludden, P.W. (1999). Ni²⁺ transport and accumulation in Rhodospirillum rubrum. J. Bacteriol. 181, 4554–4560.10.1128/JB.181.15.4554-4560.1999Search in Google Scholar PubMed PubMed Central

Wu, M., Ren, Q.H., Durkin, A.S., Daugherty, S.C., Brinkac, L.M., Dodson, R.J., Madupu, R., Sullivan, S.A., Kolonay, J.F., Nelson, W.C., et al. (2005). Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 1, 563–574.10.1371/journal.pgen.0010065Search in Google Scholar PubMed PubMed Central

Zhou, T.Q., Radaev, S., Rosen, B.P., and Gatti, D.L. (2000). Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump. EMBO J. 19, 4838–4845.10.1093/emboj/19.17.4838Search in Google Scholar PubMed PubMed Central