Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 10, 2010, Pages 2369-2384

  Nagao, Chioko ^a   Nagano, Nozomi ^b,c   Mizuguchi, Kenji ^a  

^a NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Active sites; Aldolase class I; Catalytic mechanism; Clustering; Ligand binding sites; TIM barrel glycosidases; Hydrolases

Indexed keywords

COLLAGENASE; FRUCTOSE BISPHOSPHATE ALDOLASE; GLYCOSIDASE; HYDROLASE; NUCLEOSIDE TRIPHOSPHATE; PEPTIDASE; PHOSPHORIBOSYL PYROPHOSPHATE; AMINO ACID; ENZYME; LIGAND;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; ENZYME ACTIVATION; ENZYME ACTIVE SITE; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; ALGORITHM; BINDING SITE; BIOCATALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; EXPERT SYSTEM; METABOLISM; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; BIOCATALYSIS; CATALYTIC DOMAIN; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYMES; EXPERT SYSTEMS; LIGANDS; MODELS, MOLECULAR; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 77955790190     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22750     Document Type: Article

References (66)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
2. 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;25:3389-3402.
3. Webb EC, NC-IUBMB. Enzyme Nomenclature, Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. San Diego, CA: Academic Press; 1992.
4. Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001;307:1113-1143.
5. Tian W, Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 2003;333:863-882.
6. Addou S, Rentzsch R, Lee D, Orengo CA. Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer. J Mol Biol 2009;387:416-430.
7. Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y. Automatic prediction of protein function. Cell Mol Life Sci 2003;60:2637-2650.
8. Cammer SA, Hoffman BT, Speir JA, Canady MA, Nelson MR, Knutson S, Gallina M, Baxter SM, Fetrow JS. Structure-based active site profiles for genome analysis and functional family subclassification. J Mol Biol 2003;334:387-401.
9. Audit B, Levy ED, Gilks WR, Goldovsky L, Ouzounis CA. CORRIE: enzyme sequence annotation with confidence estimates. BMC Bioinformatics 2007;8 Suppl. 4: S3.
10. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE 2009;4: e4345.
11. Brown DP, Krishnamurthy N, Sjolander K. Automated protein subfamily identification and classification. PLoS Comput Biol 2007;3: e160.
12. Wang K, Samudrala R. FSSA: a novel method for identifying functional signatures from structural alignments. Bioinformatics 2005;21:2969-2977.
13. Xie L, Bourne PE. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci USA 2008;105:5441-5446.
14. Innis CA, Anand AP, Sowdhamini R. Prediction of functional sites in proteins using conserved functional group analysis. J Mol Biol 2004;337:1053-1068.
15. del Sol Mesa A, Pazos F, Valencia A. Automatic methods for predicting functionally important residues. J Mol Biol 2003;326:1289-1302.
16. Mihalek I, Res I, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 2004;336:1265-1282.
17. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. InterProScan: protein domains identifier. Nucleic Acids Res 2005;33: W116-W120.
18. Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJ. The 20 years of PROSITE. Nucleic Acids Res 36: D245-D249, 2008.
19. Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell AL, Moulton G, Nordle A, Paine K, Taylor P, Uddin A, Zygouri C. PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 2003;31:400-402.
20. Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol 2009;387:451-464.
21. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry 2006;45:2545-2555.
22. Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005;33: W89-W93.
23. Ota M, Kinoshita K, Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J Mol Biol 2003;327:1053-1064.
24. Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 2001;307:1487-1502.
25. Wass MN, Sternberg MJ. ConFunc-functional annotation in the twilight zone. Bioinformatics 2008;24:798-806.
26. Hannenhalli SS, Russell RB. Analysis and prediction of functional subtypes from protein sequence alignments. J Mol Biol 2000;303:61-76.
27. Pazos F, Sternberg MJ. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA 2004;101:14754-14759.
28. Sankararaman S, Kolaczkowski B, Sjolander K. INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Res 2009;37: W390-W395.
29. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
30. Nagano N. EzCatDB: the enzyme catalytic-mechanism database. Nucleic Acids Res 2005;33: D407-D412.
31. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
32. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucleic Acids Res 2003;31:365-370.
33. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
34. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP. JOY: protein sequence-structure representation and analysis. Bioinformatics 1998;14:617-623.
35. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-134.
36. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. MUSTANG: a multiple structural alignment algorithm. Proteins 2006;64:559-574.
37. Dayhoff MO. Atlas of protein sequence and structure. Washington, DC: National Biomedical Research Foundation; 1979.
38. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989;5:164-166.
39. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
40. Klein P, Kanehisa M, DeLisi C. Prediction of protein function from sequence properties. Discriminant analysis of a data base. Biochim Biophys Acta 1984;787:221-226.
41. Chothia C. Structural invariants in protein folding. Nature 1975;254:304-308.
42. Ward JH. Hierarchical grouping to optimize an objective function. J Am Stat Assoc 1963;58:236-244.
43. Defays D. An efficient algorithm for a complete link method. Comput J 1977;20:364-366.
44. Sibson R. SLINK: an optimally efficient algorithm for the Single-Link Cluster Method. Comput J 1973;16:30-34.
45. Ihaka R, Gentleman R. R: a language for data analysis and graphics. J comput Graph Stat 1996;5:299-314.
46. Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene 2008;407:199-215.
47. Gerlt JA, Raushel FM. Evolution of function in (beta/alpha) 8-barrel enzymes. Curr Opin Chem Biol 2003;7:252-264.
48. Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002;321:741-765.
49. Wilmanns M, Hyde CC, Davies DR, Kirschner K, Jansonius JN. Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry 1991;30:9161-9169.
50. Shulami S, Furdui C, Adir N, Shoham Y, Anderson KS, Baasov T. A reciprocal single mutation affects the metal requirement of 3-deoxy-D-manno-2- octulosonate-8-phosphate (KDO8P) synthases from Aquifex pyrophilus and Escherichia coli. J Biol Chem 2004;279:45110-45120.
51. Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 2000;289:1546-1550.
52. Davies G, Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure 1995;3:853-859.
53. Nagano N, Porter CT, Thornton JM. The (betaalpha) (8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Eng 2001;14:845-855.
54. Watanabe T, Ishibashi A, Ariga Y, Hashimoto M, Nikaidou N, Sugiyama J, Matsumoto T, Nonaka T. Trp122 and Trp134 on the surface of the catalytic domain are essential for crystalline chitin hydrolysis by Bacillus circulans chitinase A1. FEBS Lett 2001;494:74-78.
55. Przylas I, Tomoo K, Terada Y, Takaha T, Fujii K, Saenger W, Strater N. Crystal structure of amylomaltase from thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. J Mol Biol 2000;296:873-886.
56. Czjzek M, Cicek M, Zamboni V, Burmeister WP, Bevan DR, Henrissat B, Esen A. Crystal structure of a monocotyledon (maize ZMGlu1) beta-glucosidase and a model of its complex with pnitrophenyl beta-D-thioglucoside. Biochem J 2001;354(Pt 1):37-46.
57. Ohtaki A, Mizuno M, Tonozuka T, Sakano Y, Kamitori S. Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism. J Biol Chem 2004;279:31033-31040.
58. van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L. Properties and applications of starch-converting enzymes of the alpha-amylase family. J Biotechnol 2002;94:137-155.
59. Cutfield SM, Davies GJ, Murshudov G, Anderson BF, Moody PC, Sullivan PA, Cutfield JF. The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases. J Mol Biol 1999;294:771-783.
60. Charnock SJ, Spurway TD, Xie H, Beylot MH, Virden R, Warren RA, Hazlewood GP, Gilbert HJ. The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved. J Biol Chem 1998;273:32187-32199.
61. Moreau A, Shareck F, Kluepfel D, Morosoli R. Alteration of the cleavage mode and of the transglycosylation reactions of the xylanase A of Streptomyces lividans 1326 by site-directed mutagenesis of the Asn173 residue. Eur J Biochem 1994;219:261-266.
62. Nardini M, Dijkstra BW. Alpha/beta hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 1999;9:732-737.
63. Holmquist M. Alpha/beta-hydrolase fold enzymes: structures, functions and mechanisms. Curr Protein Pept Sci 2000;1:209-235.
64. Bugg TD. Diverse catalytic activities in the alphabeta-hydrolase family of enzymes: activation of H2O. HCN, H2O2, and O2 Bioorg Chem 2004;32:367-375.
65. Leipe DD, Koonin EV, Aravind L. Evolution and classification of P-loop kinases and related proteins. J Mol Biol 2003;333:781-815.
66. Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 2008;24:719-720.