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Original Articles

Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii

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References

  • Baskaya, F. S.; Zhao, X.; Flickinger, M. C.; Wang, P. Thermodynamic Feasibility of Enzymatic Reduction of Carbon Dioxide to Methanol. Appl. Biochem. Biotechnol. 2010, 162, 391–398. DOI: 10.1007/s12010-009-8758-x.
  • Balaraman, E.; Gunanathan, C.; Zhang, J.; Shimon, L. J. W.; Milstein, D. Efficient Hydrogenation of Organic Carbonates, Carbamates and Formates Indicates Alternative Routes to Methanol Based on CO2 and CO. Nat. Chem. 2011, 3, 609–614. DOI: 10.1038/nchem.1089.
  • Li, F.-F.; Liu, S.; Cui, B.; Lau, J.; Stuart, J.; Wang, B.; Licht, S. A One-Pot Synthesis of Hydrogen and Carbon Fuels from Water and Carbon Dioxide. Adv. Energy Mater. 2015, 5, 1401791. DOI: 10.1002/aenm.201401791.
  • Angermayr, S. A.; Van Der Woude, A. D.; Correddu, D.; Vreugdenhil, A.; Verrone, V.; Hellingwerf, K. J. Exploring Metabolic Engineering Design Principles for the Photosynthetic Production of Lactic Acid by Synechocystis sp. PCC6803. Biotechnol. Biofuels. 2014, 7, 99. DOI: 10.1186/1754-6834-7-99.
  • Abate, S.; Arrigo, R.; Perathoner, S.; Centi, G. Role of Feed Composition on the Performances of Pd-Based Catalysts for the Direct Synthesis of H2O2. Top Catal. 2014, 57, 1208–1217. DOI: 10.1007/s11244-014-0289-1.
  • Plasseraud, L. Carbon Dioxide as Chemical Feedstock. Edited by Michele Aresta. ChemSusChem. 2010, 3, 631–632. DOI: 10.1002/cssc.201000097.
  • Wu, J.; Risalvato, F. G.; Ke, F.-S.; Pellechia, P. J.; Zhou, X.-D. Electrochemical Reduction of Carbon Dioxide I. Effects of the Electrolyte on the Selectivity and Activity with Sn Electrode. J. Electrochem. Soc. 2012, 159, F353–F359. DOI: 10.1149/2.049207jes.
  • Centi, G.; Perathoner, S. Catalysis: Role and challenges for a sustainable energy. Top. Catal. 2009, 52(8), 948–961. DOI: 10.1007/s11244-009-9245-x.
  • Schlapbach, L.; Züttel, A. Hydrogen-Storage Materials for Mobile Applications. Nature 2001, 414, 353–358. DOI: 10.1038/35104634.
  • Srikanth, S.; Alvarez-Gallego, Y.; Vanbroekhoven, K.; Pant, D. Enzymatic Electrosynthesis of Formic Acid through Carbon Dioxide Reduction in a Bioelectrochemical System: Effect of Immobilization and Carbonic Anhydrase Addition. ChemPhysChem. 2017, 18(22), 3174–3181. DOI: 10.1002/cphc.201700017.
  • Tezuka, M.; Yajima, T.; Tsuchiya, A. Electroreduction of Carbon Dioxide Catalyzed by Iron-Sulfur Cluster Compounds [Fe4S4 (SR) 4] 2. J. Am. Chem. Soc. 1982, 104, 6834–6836. DOI: 10.1021/ja00388a085.
  • Hawkins, A. S.; McTernan, P. M.; Lian, H.; Kelly, R. M.; Adams, M. W. W. Biological Conversion of Carbon Dioxide and Hydrogen into Liquid Fuels and Industrial Chemicals. Curr. Opin. Biotechnol. 2013, 24, 376–384. DOI: 10.1016/j.copbio.2013.02.017.
  • Crable, B. R.; Plugge, C. M.; McInerney, M. J.; Stams, A. J. M. Formate Formation and Formate Conversion in Biological Fuels Production. Enzyme Res. 2011, 2011, 1–8. DOI: 10.4061/2011/532536.
  • Rusching, U.; Müller, U.; Willnow, P.; Höpner, T. CO2 Reduction to Formate by NADH Catalysed by Formate Dehydrogenase from Pseudomonas oxalaticus. Eur. J. Biochem. 1976, 70, 325–330. DOI: 10.1111/j.1432-1033.1976.tb11021.x.
  • Höpner, T.; Ruschig, U.; Müller, U.; Willnow, P. Formate Dehydrogenase from Pseudomonas Oxalaticus, Methods Enzymol. 1982, 89, 531–537. DOI: 10.1016/S0076-6879(82)89092-7.
  • Parkinson, B. A.; Weaver, P. F. Photoelectrochemical Pumping of Enzymatic CO2 Reduction. Nature 1984, 309, 148–149. DOI: 10.1038/309148a0.
  • Mandler, D.; Willner, I. Photochemical Fixation of Carbon Dioxide: Enzymic Photosynthesis of Malic, Aspartic, Isocitric, and Formic Acids in Artificial Media. J. Chem. Soc. Perkin. Trans. 1988, 2, 997. DOI: 10.1039/p29880000997.
  • Miyatani, R.; Amao, Y. Bio-CO2 Fixation with Formate Dehydrogenase from Saccharomyces Cerevisiae and Water-Soluble Zinc Porphyrin by Visible Light. Biotechnol Lett. 2002, 24, 1931–1934. DOI: 10.1023/A:1020912527723.
  • Tishkov, V. I.; Popov, V. O. Catalytic Mechanism and Application of Formate Dehydrogenase. Biochem. 2004, 69, 1252–1267. DOI: 10.1007/s10541-005-0071-x.
  • Choe, H.; Joo, J. C.; Cho, D. H.; Kim, M. H.; Lee, S. H.; Jung, K. D.; Kim, Y. H. Efficient CO2-Reducing Activity of NAD-Dependent Formate Dehydrogenase from Thiobacillus sp. KNK65MA for Formate Production from CO2 Gas. PLoS One 2014, 9, 1–10. DOI: 10.1371/journal.pone.0103111.
  • Cone, E. J. General Procedure for the Isolation and Identification of 6-?.?.- and 6-?.?.-Hydroxy Metabolites of Narcotic Agonists and Antagonists with a Hydromorphone Structure. J. Chromatogr. A. 1976, 129, 355–361. DOI: 10.1016/S0021-9673(00)87795-X.
  • Almendra, M. J.; Brondino, C. D.; Gavel, O.; Pereira, A. S.; Tavares, P.; Bursakov, S.; Duarte, R.; Caldeira, J.; Moura, J. J. G.; Moura, I. Purification and Characterization of a Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas. Biochemistry. 1999, 38, 16366–16372. DOI: 10.1021/bi990069n.
  • Graentzdoerffer, A.; Rauh, D.; Pich, A.; Andreesen, J. R. Molecular and Biochemical Characterization of Two Tungsten- and Selenium-Containing Formate Dehydrogenases from Eubacterium Acidaminophilum that are Associated with Components of an Iron-Only Hydrogenase. Arch. Microbiol. 2003, 179, 116–130. DOI: 10.1007/s00203-002-0508-1.
  • Reda, T.; Barker, C. D.; Hirst, J. Reduction of the Iron-Sulfur Clusters in Mitochondrial NADH: Ubiquinone Oxidoreductase (Complex I) by EuII-DTPA, A Very Low Potential Reductant. Biochemistry. 2008, 47, 8885–8893. DOI: 10.1021/bi800437g.
  • Grimaldi, S.; Schoepp-Cothenet, B.; Ceccaldi, P.; Guigliarelli, B.; Magalon, A. The Prokaryotic Mo/W-Bispgd Enzymes Family: A Catalytic Workhorse in Bioenergetic. Biochem. Biophys. Acta. - Bioenerg. 2013, 1827, 1048–1085. DOI: 10.1016/j.bbabio.2013.01.011.
  • Tunney, J. M.; McMaster, J.; Garner, C. D. Molybdenum and Tungsten Enzymes. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering Comprehensive Coordination Chemistry II. 2003, 8, 459–477.
  • Bassegoda, A.; Madden, C.; Wakerley, D. W.; Reisner, E.; Hirst, J. Reversible Interconversion of CO2 and Formate by a Molybdenum-Containing Formate Dehydrogenase, J. Am. Chem. Soc. 2014, 136, 15473–15476. DOI: 10.1021/ja508647u.
  • Leopoldini, M.; Chiodo, S. G.; Toscano, M.; Russo, N. Reaction Mechanism of Molybdoenzyme Formate Dehydrogenase. Chem. A Eur. J. 2008, 14, 8674–8681. DOI: 10.1002/chem.200800906.
  • Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T. J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; et al. Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega. Mol. Syst. Biol. 2011, 7, 539. DOI: 10.1038/msb.2011.75.
  • EMBL. SIB Swiss Institute of Bioinformatics, Protein Information Resource (PIR), UniProt. Nucleic Acids Res. 2013, 41, D43–D47.
  • Boyington, J. C.; Gladyshev, V. N.; Khangulov, S. V.; Stadtman, T. C.; Sun, P. D. Crystal structure of formate dehydrogenase H: Catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science 1997, 275, 1305–1308. DOI: 10.1126/science.275.5304.1305.
  • Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL Workspace: A Web-Based Environment for Protein Structure Homology Modelling. Bioinformatics 2006, 22, 195–201. DOI: 10.1093/bioinformatics/bti770.
  • Juricova, H.; Videnska, P.; Lukac, M.; Faldynova, M.; Babak, V.; Havlickova, H.; Sisak, F.; Rychlik, I. Influence of Salmonella Enterica Serovar Enteritidis Infection on the Development of the Cecum Microbiota in Newly Hatched Chicks. Appl. Environ. Microbiol. 2013, 79, 745–747. DOI: 10.1128/AEM.02886-12.
  • Thauer, R. K. Carbon Dioxide Reduction to Formate by NADPH. Initial Step in the Total Synthesis of Acetate from Carbon Dioxide in Clostridium Thermoaceticum. FEBS (Fed. Eur. Biochem. Soc.) Lett. 1972, 27, 111–115. DOI: 10.1016/0014-5793(72)80421-6.
  • Scherer, P. A.; Thauer, R. K. Purification and Properties of Reduced Ferredoxin: CO2 Oxidoreductase from Clostridium pasteurianum, a Molybdenum Iron‐Sulfur‐Protein. Eur. J. Biochem. 1978, 85, 125–135. DOI: 10.1111/j.1432-1033.1978.tb12220.x.
  • da Silva, S. M.; Pimentel, C.; Valente, F. M. A.; Rodrigues-Pousada, C.; Pereira, I. A. C. Tungsten and Molybdenum Regulation of Formate Dehydrogenase Expression in Desulfovibrio vulgaris Hildenborough. J. Bacteriol. 2011, 193, 2909–2916. DOI: 10.1128/JB.00042-11.
  • Maia, L. B.; Moura, I.; Moura, J. J. G. Molybdenum and Tungsten-Containing Formate Dehydrogenases: Aiming to Inspire a Catalyst for Carbon Dioxide Utilization. Inorganica. Chim. Acta. 2017, 455, 350–363. DOI: 10.1016/j.ica.2016.07.010.
  • Raaijmakers, H. C. A.; Romão, M. J. Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation of the Crystal Structure Suggests a New Reaction Mechanism. J. Biol. Inorg. Chem. 2006, 11, 849–854. DOI: 10.1007/s00775-006-0129-2.
  • Jormakka, M.; Tornroth, S.; Byrne, B.; Iwata, S. Molecular Basis of Proton Motive Force Generation: Structure of Formate Dehydrogenase-N\r168. Science 2002, 295, 1863–1868.
  • Raaijmakers, H.; Macieira, S.; Dias, J. M.; Teixeira, S.; Bursakov, S.; Huber, R.; Moura, J. J. G.; Moura, I.; Romão, M. J. Gene Sequence and the 1.8 Å Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas. Structure 2002, 10, 1261–1272. DOI: 10.1016/S0969-2126(02)00826-2.
  • Gladyshev, V. N.; Khangulov, S. V.; Axley, M. J.; Stadtman, T. C. Coordination of Selenium to Molybdenum in Formate Dehydrogenase H from Escherichia Coli. Proc. Natl. Acad. Sci. U S A. 1994, 91, 7708–7711. DOI: 10.1073/pnas.91.16.7708.
  • Sancak, Y.; Markhard, A. L.; Kitami, T.; Kovács-Bogdán, E.; Kamer, K. J.; Udeshi, N. D.; Carr, S. A.; Chaudhuri, D.; Clapham, D. E.; Li, A. A.; et al. EMRE is an Essential Component of the Mitochondrial Calcium Uniporter Complex. Science 2013, 342, 1379–1382. DOI: 10.1126/science.1242993.
  • Schuchmann, K.; Vonck, J.; Müller, V. A Bacterial Hydrogen-Dependent CO2 Reductase forms Filamentous Structures. FEBS J. 2016, 283, 1311–1322. DOI: 10.1111/febs.13670.
  • Costa, C.; Teixeira, M.; LeGall, J.; Moura, J. J. G.; Moura, I. Formate Dehydrogenase from Desulfovibrio desulfuricans ATCC 27774: Isolation and Spectroscopic Characterization of the Active Sites (Heme, Iron- Sulfur Centers and Molybdenum). J. Biol. Inorg. Chem. 1997, 2, 198–208. DOI: 10.1007/s007750050125.
  • Maia, L. B.; Fonseca, L.; Moura, I.; Moura, J. J. G. Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study. J. Am. Chem. Soc. 2016, 138, 8834–8846. DOI: 10.1021/jacs.6b03941.
  • Schrapers, P.; Hartmann, T.; Kositzki, R.; Dau, H.; Reschke, S.; Schulzke, C.; Leimkühler, S.; Haumann, M. Sulfido and Cysteine Ligation Changes at the Molybdenum Cofactor During Substrate Conversion by Formate Dehydrogenase (fdh) from Rhodobacter capsulatus, Inorg. Chem. 2015, 54, 3260–3271. DOI: 10.1021/ic502880y.
  • Hartmann, T.; Schrapers, P.; Utesch, T.; Nimtz, M.; Rippers, Y.; Dau, H.; Mroginski, M. A.; Haumann, M.; Leimkühler, S. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions. Biochemistry 2016, 55, 2381–2389. DOI: 10.1021/acs.biochem.6b00002.
  • Hartmann, T.; Leimkühler, S. The Oxygen-Tolerant and NAD+-Dependent Formate Dehydrogenase from Rhodobacter capsulatus is Able to Catalyze the Reduction of CO2 to Formate. FEBS J. 2013, 280, 6083–6096. DOI: 10.1111/febs.12528.
  • Bursakov, S.; Liu, M. Y.; Payne, W. J.; LeGall, J.; Moura, I.; Moura, J. J. G. Isolation and Preliminary Characterization of a Soluble Nitrate Reductase from the Sulfate-Reducing Organism Desulfovibrio desulfuricans ATCC 27774. Anaerobe 1995, 1, 55–60. DOI: 10.1016/S1075-9964(95)80444-7.
  • Sebban, C.; Blanchard, L.; Bruschi, M.; Guerlesquin, F. Purification and Characterization of the Formate Dehydrogenase from Desulfovibrio vulgaris Hildenborough. FEMS Microbiol. Lett. 1995, 133, 143–149. DOI: 10.1111/J.1574-6968.1995.Tb07875.X.
  • Heidelberg, J. F.; Seshadri, R.; Haveman, S. A.; Hemme, C. L.; Paulsen, I. T.; Kolonay, J. F.; Eisen, J. A.; Ward, N.; Methe, B.; Brinkac, L. M.; et al. The Genome Sequence of the Anaerobic, Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Nat. Biotechnol. 2004, 22, 554–559. DOI: 10.1038/nbt959.
  • Martins, M.; Mourato, C.; Pereira, I. A. C. Desulfovibrio vulgaris Growth Coupled to Formate-Driven H2Production. Environ. Sci. Technol. 2015, 49, 14655–14662. DOI: 10.1021/acs.est.5b02251.
  • Schauer, N. L.; Ferry, J. G. Properties of Formate Dehydrogenase in Methanobacterium formicicum. J. Bacteriol. 1982, 150, 1–7.
  • Barber, M. J.; Siegel, L. M.; Schauer, N. L.; May, H. D.; Ferry, J. G. Formate Dehydrogenase From Methanobacterium formicicum - Electron-Paramagnetic Resonance Spectroscopy of the Molybdenum and Iron-Sulfur Centers. J. Biol. Chem. 1983, 258, 839–845. http://www.ncbi.nlm.nih.gov/pubmed/6309816%5Cnhttp://apps.webofknowledge.com//full_record.do?product=UA&search_mode=GeneralSearch&qid=11&SID=1BAmv99aRMXdjhP6SK4&page=1&doc=1%5CnAll Papers/B/Barber et al. 1983 - Formate dehydrogenase from Methanobacterium.
  • Shuber, A. P.; Orr, E. C.; Recny, M. A.; Schendel, P. F.; May, H. D.; Schauer, N. L.; Ferry, J. G. Cloning, Expression, and Nucleotide Sequence of the Formate Dehydrogenase Genes from Methanobacterium formicicum. J. Biol. Chem. 1986, 261, 12942–12947.
  • Johnson, J. L.; Bastian, N. R.; Schauer, N. L.; Ferry, J. G.; Rajagopalan, K. V. Identification of Molybdopterin Guanine Dinucleotide in Formate Dehydrogenase from Methanobacterium formicicum. FEMS Microbiol. Lett. 1991, 77, 213–216. DOI: 10.1111/j.1574-6968.1991.tb04350.x.
  • Nölling, J.; Reeve, J. N. Growth- and Substrate-Dependent Transcription of the Formate Dehydrogenase (fdhCAB) Operon in Methanobacterium Thermoformicicum Z-245. J. Bacteriol. 1997, 179, 899–908. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC178775/.
  • Jollie, D. R.; Lipscomb, J. D. Formate Dehydrogenase from Methylosinus trichosporium OB3b. Purification and Spectroscopic Characterization of the Cofactors. J. Biol. Chem. 1991, 266, 21853–21863. DOI: 10.1016/0076-6879(90)88051-B.
  • Xin, J.; Zhang, Y.; Zhang, S.; Xia, C.; Li, S. Methanol Production from CO2 by Resting Cells of the Methanotrophic Bacterium Methylosinus trichosporium IMV 3011, J Basic Microbiol. 2007, 47, 426–435. DOI: 10.1002/jobm.200710313.
  • D. Niks, J. Duvvuru, M. Escalona, R. Hille, Spectroscopic and Kinetic Properties of the Molybdenum-Containing, NAD+-Dependent Formate Dehydrogenase from Ralstonia eutropha. J. Biol. Chem. 2016, 291, 1162–1174. DOI: 10.1074/jbc.M115.688457.
  • Friedebold, J.; Bowien, B. Physiological and Biochemical Characterization of the Soluble Formate Dehydrogenase, a Molybdoenzyme from Alcaligenes eutrophus. J. Bacteriol. 1993, 175, 4719–4728. DOI: 10.1128/jb.175.15.4719-4728.1993.
  • Oh, J.-I. Structural Analysis of the fds Operon Encoding the NAD+-Linked Formate Dehydrogenase of Ralstonia eutropha. J. Biol. Chem. 1998, 273, 26349–26360. DOI: 10.1074/jbc.273.41.26349.

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