A tale of two ferredoxins: Sequence similarity and structural differences

BMC Structural Biology

Volumn 6, Issue , 2006, Pages

  Sri Krishna, S ^b,c   Sadreyev, Ruslan I ^a   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FERREDOXIN; PYRUVATE SYNTHASE;

ARTICLE; CLUSTER ANALYSIS; HYDROPHOBICITY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DESULFOVIBRIO; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; FERREDOXINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

BACTERIA (MICROORGANISMS);

EID: 33646472273     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-8     Document Type: Article

References (37)

1. Chothia C: Proteins. One thousand families for the molecular biologist. Nature 1992, 357(6379):543-544.
2. Wolf YI, Grishin NV, Koonin EV: Estimating the number of protein folds and families from complete genome data. J Mol Biol 2000, 299(4):897-905.
3. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
4. Doolittle RF: Similar amino acid sequences: chance or common ancestry? Science 1981, 214(4517):149-159.
5. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
6. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85(8):2444-2448.
7. Karlin S, Altschul SF: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A 1990, 87(6):2264-2268.
8. Grishin NV: Fold change in evolution of protein structures. J Struct Biol 2001, 134(2-3):167-185.
9. Grishin NV: KH domain: one motif, two folds. Nucleic Acids Res 2001, 29(3):638-643.
10. Lupas AN, Ponting CP, Russell RB: On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 2001, 134(2-3):191-203.
11. Murzin AG: How far divergent evolution goes in proteins. Curr Opin Struct Biol 1998, 8(3):380-387.
12. Siomi H, Matunis MJ, Michael WM, Dreyfuss G: The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res 1993, 21(5):1193-1198.
13. Doolittle RF: Convergent evolution: the need to be explicit. Trends Biochem Sci 1994, 19(1):15-18.
14. Doolittle RF: Similar amino acid sequences revisited. Trends Biochem Sci 1989, 14(7):244-245.
15. George DG, Hunt LT, Yeh LS, Barker WC: New perspectives on bacterial ferredoxin evolution. J Mol Evol 1985, 22(1):20-31.
16. Bruschi M, Guerlesquin F: Structure, function and evolution of bacterial ferredoxins. FEMS Microbiol Rev 1988, 4(2):155-175.
17. Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC: Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Biol 1999, 6(2):182-190.
18. Iverson TM, Luna-Chavez C, Croal LR, Cecchini G, Rees DC: Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J Biol Chem 2002, 277(18):16124-16130.
19. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14(9):755-763.
20. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucleic Acids Res 2004, 32 Database issue:D138-41.
21. Gouet P, Chinardet N, Welch M, Guillet V, Cabantous S, Birck C, Mourey L, Samama JP: Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY - CheA(124 - 257) complex. Acta Crystallogr D Biol Crystallogr 2001, 57(Pt 1):44-51.
22. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 2004, 32 Database issue:D226-9.
23. Harutyunyan EH, Safonova TN, Kuranova IP, Popov AN, Teplyakov AV, Obmolova GV, Rusakov AA, Vainshtein BK, Dodson GG, Wilson JC, Perutz MF: The structure of deoxy- and oxy-leghaemoglobin from lupin. J Mol Biol 1995, 251(1):104-115.
24. Darimont B, Sterner R: Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima. Embo J 1994, 13(8):1772-1781.
25. Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313(4):903-919.
26. Iverson TM, Luna-Chavez C, Schroder I, Cecchini G, Rees DC: Analyzing your complexes: structure of the quinol-fumarate reductase respiratory complex. Curr Opin Struct Biol 2000, 10(4):448-455.
27. Hederstedt L: Respiration without O2. Science 1999, 284(5422):1941-1942.
28. Hagerhall C: Succinate: quinone oxidoreductases. Variations on a conserved theme. Biochim Biophys Acta 1997, 1320(2):107-141.
29. Beinert H: Iron-sulfur proteins: ancient structures, still full of surprises. J Biol Inorg Chem 2000, 5(1):2-15.
30. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ: InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002, 3(3):225-235.
31. Dobritzsch D, Schneider G, Schnackerz KD, Lindqvist Y: Crystal structure of dihydropyrimidine dehydrogenase, a major determinant of the pharmacokinetics of the anti-cancer drug 5-fluorouracil. Embo J 2001, 20(4):650-660.
32. Heger A, Holm L: Exhaustive enumeration of protein domain families. J Mol Biol 2003, 328(3):749-767.
33. Lo Surdo P, Walsh MA, Sollazzo M: A novel ADP- and zinc-binding fold from function-directed in vitro evolution. Nat Struct Mol Biol 2004, 11(4):382-383.
34. Krishna SS, Grishin NV: Structurally analogous proteins do exist! Structure (Camb) 2004, 12(7):1125-1127.
35. Pfam::. [http://pfam.wustl.edu/hmmsearch.shtml].
36. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC: X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 1998, 282(5395):1853-1858.
37. Esnouf RM: Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr D Biol Crystallogr 1999, 55 (Pt 4):938-940.