A radical solution for the biosynthesis of the H-cluster of hydrogenase

FEBS Letters

Volumn 580, Issue 2, 2006, Pages 363-367

  Peters, John W ^a   Szilagyi, Robert K ^a   Naumov, Anatoli ^a   Douglas, Trevor ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

H cluster biosynthesis; Hydrogenase; Prebiotic chemistry; Radical SAM

Indexed keywords

CARBON MONOXIDE; CYANIDE; GLYCINE; HYDROGENASE; IRON; S ADENOSYLMETHIONINE;

ARTICLE; DECOMPOSITION; DENSITY FUNCTIONAL THEORY; ENZYME SYNTHESIS; GENE CLUSTER; HYDE GENE; HYDF GENE; HYDG GENE; PRIORITY JOURNAL; PROTEIN EXPRESSION;

BINDING SITES; CARBON MONOXIDE; CYANIDES; GLYCINE; HYDROGENASE; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 30644471959     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.12.040     Document Type: Article

References (36)

1. P.M. Vignais, and B. Billoud Meyer J: Classification and phylogeny of hydrogenases FEMS Microbiol. Rev. 25 2001 455 501
2. M.W. Adams The structure and mechanism of iron-hydrogenases Biochim. Biophys. Acta 1020 1990 115 145
3. M. Wolin Interaction between H2-producing and methane-producing species H. Schelgel G. Gottschalk N. Pfennig Microbial Production and Utlization of Gases 1976 Akademie der Wissenshaften 141 150
4. R.P. Happe, and W. Roseboom Unusual FTIR and EPR properties of the H2-activating site of the cytoplasmic NAD-reducing hydrogenase from Ralstonia eutropha FEBS Lett. 466 2000 259 263
5. A.J. Pierik, and M. Hulstein A low-spin iron with CN and CO as intrinsic ligands forms the core of the active site in [Fe]-hydrogenases Eur. J. Biochem. 258 1998 572 578
6. A. Volbeda, and M.H. Charon Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas Nature 373 1995 580 587
7. Y. Nicolet, and C. Cavazza Fe-only hydrogenases: structure, function and evolution J. Inorg. Biochem. 91 2002 1 8
8. Y. Nicolet, and C. Piras Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center Struct. Fold. Des. 7 1999 13 23
9. J.W. Peters, and W.N. Lanzilotta X-ray crystal structure of the Fe-only hydrogenase CpI from Clostridium pasteurianum to 1.8 angstrom resolution Science 282 1998 1853 1858
10. Y. Nicolet, and A.L. de Lacey Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans J. Am. Chem. Soc. 123 2001 1596 1601
11. S. Reissmann, and E. Hochleitner Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands Science 299 2003 1067 1070
12. M.C. Posewitz, and P.W. King Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase J. Biol. Chem. 279 2004 25711 25720
13. J.K. Rubach, and X. Brazzolotto Biochemical characterization of the HydE and HydG iron-only hydrogenase maturation enzymes from Thermatoga maritima FEBS Lett. 579 2005 5055 5060
14. M. Fontecave, and E. Mulliez Adenosylmethionine as a source of 5′-deoxyadenosyl radicals Curr. Opin. Chem. Biol. 5 2001 506 511
15. P.A. Frey Radical mechanisms of enzymatic catalysis Annu. Rev. Biochem. 2001 70 2004 121 148
16. H.J. Sofia, and G. Chen Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods Nucleic Acids Res. 29 2001 1097 1106
17. C.J. Walsby, and D. Ortillo An anchoring role for FeS clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme J. Am. Chem. Soc. 124 2002 11270 11271
18. J.R. Miller, and R.W. Busby Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein Biochemistry 39 2000 15166 15178
19. E.C. Duin, and M.E. Lafferty [2Fe-2S] to [4Fe-4S] cluster conversion in Escherichia coli biotin synthase Biochemistry 36 1997 11811 11820
20. R. Kulzer, and T. Pils Reconstitution and characterization of the polynuclear iron-sulfur cluster in pyruvate formate-lyase-activating enzyme. Molecular properties of the holoenzyme form J. Biol. Chem. 273 1998 4897 4903
21. R.M. Cicchillo, and S.J. Booker Mechanistic investigations of lipoic acid biosynthesis in Escherichia coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl synthase polypeptide J. Am. Chem. Soc. 127 2005 2860 2861
22. D.C. Johnson, and D.R. Dean Structure, function, and formation of biological iron-sulfur clusters Annu. Rev. Biochem. 74 2005 247 281
23. R.M. Allen, and R. Chatterjee Biosynthesis of the iron-molybdenum cofactor of nitrogenase Crit. Rev. Biotechnol. 14 1994 225 249
24. M. Bruschi, and G. Zampella DFT investigations of models related to the active site of [NiFe] and [Fe] hydrogenases Coord. Chem. Rev. 249 2005 1620 1640
25. I.P. Georgakaki, and L.M. Thomson Fundamental properties of small molecule models of Fe-only hydrogenase: computations relative to the definition of an entatic state in the active site Coord. Chem.Rev. 238 2003 255 266
26. Z.P. Liu, and P. Hu Mechanism of H-2 metabolism on Fe-only hydrogenases J. Chem. Phys. 117 2002 8177 8180
27. T.J. Zhou, and Y.R. Mo Density functional study on dihydrogen activation at the H cluster in Fe-only hydrogenases Inorg. Chem. 44 2005 4941 4946
28. A.D. Becke Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 38 1988 3098 3100
29. J.P. Perdew Density-functional approximation for the correlation energy of the inhomogeneous electron gas Phys. Rev. B 33 1986 8822 8824
30. W.R. Wadt, and P.J. Hay Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Na to Bi J. Chem. Phys. 82 1985 284 298
31. M.J.T. Frisch, and G.W. Schlegel Gaussian03, Revision C02 2004 Gaussian, Inc Pittsburgh, PA
32. J. Tomasi, and M. Persico Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent Chem. Rev. 94 1994 2027 2094
33. G.D. Cody, and N.Z. Boctor Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate Science 289 2000 1337 1340
34. M. Dorr, and J. Kassbohrer A possible prebiotic formation of ammonia from dinitrogen on iron sulfide surfaces Angew. Chem. Int. Ed. 42 2003 1540 1543
35. G. Wachtershauser Groundworks for an evolutionary biochemistry: the iron-sulphur world Prog. Biophys. Mol. Biol. 58 1992 85 201
36. F. Berkovitch, and Y. Nicolet Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme Science 303 2004 76 79