Functional insights from the structural modelling of a small Fe-hydrogenase

Biochemical and Biophysical Research Communications

Volumn 339, Issue 1, 2006, Pages 277-283

  Tosatto, Silvio C E ^a   Giacometti, Giorgio M ^a   Valle, Giorgio ^a   Costantini, Paola ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

Biohydrogen; Fold recognition; Function prediction; H cluster; hydA

Indexed keywords

HYDROGENASE;

ARTICLE; BACTERIAL STEM CANKER; BIOINFORMATICS; CATALYSIS; CHEMICAL MODEL; ENTEROBACTER CLOACAE; ENZYME ACTIVITY; ENZYME INACTIVATION; ENZYME STRUCTURE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENTEROBACTER CLOACAE; HYDROGENASE; IRON-SULFUR PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ENTEROBACTER CLOACAE;

EID: 28144455425     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2005.11.012     Document Type: Article

References (41)

1. M. Stephenson, and L.H. Stickland Hydrogenases: a bacterial enzyme activating molecular hydrogen I. The properties of the enzyme Biochem. J. 25 1931 205 214
2. A. Volbeda, M.H. Charon, C. Piras, E.C. Hatchikian, M. Frey, and J.C. Fontecilla-Camps Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas Nature 373 1995 580 587
3. E. Garcin, X. Vernede, E.C. Hatchikian, A. Volbeda, M. Frey, and J.C. Fontecilla-Camps The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center Structure Fold Des. 7 1999 557 566
4. M.W. Adams The structure and mechanism of iron-hydrogenases Biochim. Biophys. Acta 1020 1990 115 145
5. A. Berkessel, and R.K. Thauer On the mechanism of catalysis by a metal-free hydrogenase from methanogenic archaea: enzymic transformation without a metal Angew. Chem. Int. 34 1995 2247 2250
6. M. Frey Hydrogenases: hydrogen-activating enzymes Chembiochem 3 2002 153 160
7. P.M. Vignais, B. Billoud, and J. Meyer Classification and phylogeny of hydrogenases FEMS Microbiol. Rev. 25 2001 455 501
8. P. Tamagnini, R. Axelsson, P. Lindberg, F. Oxelfelt, R. Wunschiers, and P. Lindblad Hydrogenases and hydrogen metabolism of cyanobacteria Microbiol. Mol. Biol. Rev. 66 2002 1 20 table of contents
9. M.W. Adams, and E.I. Stiefel Organometallic iron: the key to biological hydrogen metabolism Curr. Opin. Chem. Biol. 4 2000 214 220
10. T. Happe, and A. Kaminski Differential regulation of the Fe-hydrogenase during anaerobic adaptation in the green alga Chlamydomonas reinhardtii Eur. J. Biochem. 269 2002 1022 1032
11. Y. Nicolet, C. Piras, P. Legrand, C.E. Hatchikian, and J.C. Fontecilla-Camps Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center Structure Fold. Des. 7 1999 13 23
12. J.W. Peters, W.N. Lanzilotta, B.J. Lemon, and L.C. Seefeldt X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution Science 282 1998 1853 1858
13. C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi, L. De Gioia, S.C. Davies, X. Yang, L.S. Wang, G. Sawers, and C.J. Pickett Synthesis of the H-cluster framework of iron-only hydrogenase Nature 433 2005 610 613
14. M.C. Posewitz, P.W. King, S.L. Smolinski, L. Zhang, M. Seibert, and M.L. Ghirardi Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase J. Biol. Chem. 279 2004 25711 25720
15. H.J. Sofia, G. Chen, B.G. Hetzler, J.F. Reyes-Spindola, and N.E. Miller 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
16. J. Mishra, S. Khurana, N. Kumar, A.K. Ghosh, and D. Das Molecular cloning, characterization, and overexpression of a novel [Fe]-hydrogenase isolated from a high rate of hydrogen producing Enterobacter cloacae IIT-BT 08 Biochem. Biophys. Res. Commun. 324 2004 679 685
17. K.D. Pruitt, T. Tatusova, and D.R. Maglott NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 33 2005 D501 D504 Database issue
18. N.J. Mulder, R. Apweiler, T.K. Attwood, A. Bairoch, D. Barrell, A. Bateman, D. Binns, M. Biswas, P. Bradley, P. Bork, P. Bucher, R.R. Copley, E. Courcelle, U. Das, R. Durbin, L. Falquet, W. Fleischmann, S. Griffiths-Jones, D. Haft, N. Harte, N. Hulo, D. Kahn, A. Kanapin, M. Krestyaninova, R. Lopez, I. Letunic, D. Lonsdale, V. Silventoinen, S.E. Orchard, M. Pagni, D. Peyruc, C.P. Ponting, J.D. Selengut, F. Servant, C.J. Sigrist, R. Vaughan, and E.M. Zdobnov The InterPro Database, 2003 brings increased coverage and new features Nucleic Acids Res. 31 2003 315 318
19. A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S.R. Eddy, S. Griffiths-Jones, K.L. Howe, M. Marshall, and E.L. Sonnhammer The Pfam protein families database Nucleic Acids Res. 30 2002 276 280
20. N. Hulo, C.J. Sigrist, V. Le Saux, P.S. Langendijk-Genevaux, L. Bordoli, A. Gattiker, E. De Castro, P. Bucher, and A. Bairoch Recent improvements to the PROSITE database Nucleic Acids Res. 32 2004 D134 D137 Database issue
21. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
22. M. Albrecht, S.C.E. Tosatto, T. Lengauer, and G. Valle Simple consensus procedures are effective and sufficient in secondary structure prediction Protein Eng. 16 2003 459 462
23. J.M. Bujnicki, A. Elofsson, D. Fischer, and L. Rychlewski Structure prediction meta server Bioinformatics 17 2001 750 751
24. K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski 3D-Jury: a simple approach to improve protein structure predictions Bioinformatics 19 2003 1015 1018
25. L. Rychlewski, L. Jaroszewski, W. Li, and A. Godzik Comparison of sequence profiles. Strategies for structural predictions using sequence information Protein Sci. 9 2000 232 241
26. E. Bindewald, A. Cestaro, J. Hesser, M. Heiler, and S.C. Tosatto MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification Protein Eng. 16 2003 785 789
27. P. Fontana, E. Bindewald, S. Toppo, R. Velasco, G. Valle, and S.C. Tosatto The SSEA server for protein secondary structure alignment Bioinformatics 21 2005 393 395
28. A. Andreeva, D. Howorth, S.E. Brenner, T.J. Hubbard, C. Chothia, and A.G. Murzin SCOP database in 2004: refinements integrate structure and sequence family data Nucleic Acids Res. 32 2004 D226 D229 Database issue
29. F.M. Pearl, C.F. Bennett, J.E. Bray, A.P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, and C.A. Orengo The CATH database: an extended protein family resource for structural and functional genomics Nucleic Acids Res. 31 2003 452 455
30. C. Notredame, D.G. Higgins, and J. Heringa T-Coffee: a novel method for fast and accurate multiple sequence alignment J. Mol. Biol. 302 2000 205 217
31. S.C.E. Tosatto, E. Bindewald, J. Hesser, and R. Männer A divide and conquer approach to fast loop modeling Protein Eng. 15 2002 279 286
32. A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 12 2003 2001 2014
33. S.C.E. Tosatto The victor/FRST function for model quality estimation J. Comput. Biol. 12 2005 1316 1327
34. H.M. Berman, T. Battistuz, T.N. Bhat, W.F. Bluhm, P.E. Bourne, K. Burkhardt, Z. Feng, G.L. Gilliland, L. Iype, S. Jain, P. Fagan, J. Marvin, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J.D. Westbrook, and C. Zardecki The protein data bank Acta Crystallogr. D. Biol. Crystallogr. 58 2002 899 907
35. J. Heringa, and W.R. Taylor Three-dimensional domain duplication, swapping and stealing Curr. Opin. Struct. Biol. 7 1997 416 421
36. L.N. Kinch, and N.V. Grishin Evolution of protein structures and functions Curr. Opin. Struct. Biol. 12 2002 400 408
37. N.V. Grishin Fold change in evolution of protein structures J. Struct. Biol. 134 2001 167 185
38. E. Van Niel, M.A. Buddle, G. de Haas, F.J. van der Wal, P. Claassen, and A.J.M. Stams Distinctive properties of high hydrogen producing extreme thermophiles, Caldicellulosiruptor saccharolyticus and Thermotoga elfii Int. J. Hydrogen Energ. 27 2002 1391 1398
39. A. Kumar, and D. Das Enhancement of production by Enterobacter cloacae IIT-BT 08 Process Biochem. 35 2000 589 593
40. S.A. Van Ooteghem, A. Jones, D. Van Der Lelie, B. Dong, and D. Mahajan H(2) production and carbon utilization by Thermotoga neapolitana under anaerobic and microaerobic growth conditions Biotechnol. Lett. 26 2004 1223 1232
41. M.F. Verhagen, T. O'Rourke, and M.W. Adams The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization Biochim. Biophys. Acta 1412 1999 212 229