Acta NaturaeActa Naturae2075-8251Acta Naturae Ltd1078410.32607/20758251-2009-1-3-89-93Research ArticleAtomic Resolution Crystal Structure of NAD +Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1ShabalinI G-PolyakovK M-TishkovV I-PopovV Ovpopov@inbi.ras.ruA.N. Bach Institute of Biochemistry RASV.A. Engelhardt Institute of Molecular Biology RAS1512200913899317012020Copyright © 2009, Shabalin I.G., Polyakov K.M., Tishkov V.I., Popov V.O.2009formate dehydrogenaseX-ray diffraction studyatomic resolutionenzymatic catalysisFormate dehydrogenases catalyze the oxidation of formate into carbon dioxide and can be divided into several groups based on the quaternary structure, as well as on the presence of prosthetic groups and cofactors. The structurally simplest formate dehydrogenases are NAD--dependent formate dehydrogenases (FDH, EC 1.2.1.2), which oxidize formate coupled with reduction of the coenzyme NAD- into NADH [1]: НСОО- - NAD- ↔ СО2 ↑ - NADH. Formate dehydrogenases belong to a large superfamily of D-isomer specific 2-hydroxyacid dehydrogenases [2]. Formate dehydrogenases of this type contain no metal ions or prosthetic groups in the active sites and have a high specificity towards both NAD- and formate. FDHs from different organisms (bacteria, yeast, plants) function as dimers consisting of two identical subunits with a molecular weight from 35 to 50 kDa. The molecular mechanism of FDH is characterized by the direct transfer of a hydride ion from the substrate to the C4 atom of the nicotinamide ring of NAD- without additional proton transfer steps, which usually occurs in reactions catalyzed by related NAD--dependent dehydrogenases. Hence, the FDH-catalyzed reaction is a convenient model for studying the mechanism of hydride ion transfer in the active site of NAD--dependent hydrogenases by methods of quantum mechanics and molecular dynamics [3–5].[Tishkov V.I., Popov V.O. // Biochemistry Mosc. 2004. V. 69. № 11. P. 1252.][Vinals C., Depiereux E., Feytmans E. // Biochem. Biophys. Res. Commun. 1993. V. 192. № 1. P. 182.][Bandaria J.N., Dutta S., Hill S. E., Kohen A., Cheatum C.M. // J. Am. Chem. Soc. 2008. V. 130. № 1. P. 22.][Castillo R., Oliva M., Marti S., Moliner V. // J. Phys. Chem. B. 2008. V. 112. № 32. P. 10012.][Torres R.A., Schitt B., Bruice T.C. // J. Am. Chem. Soc. 1999. V. 121. № 36. P. 8164.][Dauter Z., Lamzin V.S., Wilson K.S. // Curr. Opin. Struct. Biol. 1997. V. 7. № 5. P. 681.][Rubach J.K., Plapp B.V. // Biochemistry. 2003. V. 42. № 10. P. 2907.][Meijers R., Morris R.J., Adolph H.W., Merli A., Lamzin V.S., et al. // J. Biol. Chem. 2001. V. 276. № 12. P. 9316.][Meijers R., Adolph H.W., Dauter Z., Wilson K. S., Lamzin V.S., et al. // Biochemistry. 2007. V. 46. № 18. P. 5446.][Schlieben N.H., Niefind K., Muller J., Riebel B., Hummel W., et al. // J. Mol. Biol. 2005. V. 349. № 4. P. 801.][Cameron A., Read J., Tranter R., Winter V. J., Sessions R.B., et al. // J. Biol. Chem. 2004. V. 279. № 30. P. 31429.][Lamzin V.S., Dauter Z., Popov V.O., Harutyunyan E.H., Wilson K.S. // J. Mol. Biol. 1994. V. 236. № 3. P. 759.][Schirwitz K., Schmidt A., Lamzin V.S. // Protein Sci. 2007. V.16. № 6. P. 1146.][Shabalin I.G., Filippova E.V., Polyakov K.M., Sadykhov E.G., Safonova T.N., et al. // Acta Crystallogr. D Biol. Crystallogr. 2009. V. 65. № 12. P. 1315.][Otwinowski Z., Minor W. // Methods in enzymology. 1997. V. 276. P. 307.][Murshudov G.N., Vagin A.A., Dodson E.J. // Acta Crystallogr. D Biol. Crystallogr. 1997. V. 53. № 3. P. 240.][Emsley P., Cowtan K. // Acta Crystallogr. D Biol. Crystallogr. 2004. V. 60. № 12. P. 2126.][Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J. M. // J. Appl. Cryst. 1993. V. 26. № 2. P. 283.][Vaguine A.A., Richelle J., Wodak S.J. // Acta Crystallogr. D Biol. Crystallogr. 1999. V. 55. № 1. P. 191.][Blanchard J.S., Cleland W.W. // Biochemistry. 1980. V. 19. № 15. P. 3543.][Rotberg N.S., Cleland W.W. // Biochemistry. 1991. V. 30. № 16. P. 4068.][Popov V.O., Lamzin V.S. // Biochem. J. 1994. V. 301. № 3. P. 625.][Kahn K., Bruice T.C. // J. Am. Chem. Soc. 2001. V. 123. № 48. P. 11960.][Engh R.A., Huber R. // Acta Crystallogr. A Found. Crystallogr. 1991. V. 47. № 4. P. 392.]