Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands

BMC Structural Biology

Volumn 12, Issue , 2012, Pages

  Ueno, Keisuke ^a   Mineta, Katsuhiko ^a   Ito, Kimihito ^a   Endo, Toshinori ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

OXIDOREDUCTASE; TRANSFERASE;

AMINO ACID SEQUENCE; ARTICLE; GENE MUTATION; PARAMETERS; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN STRUCTURE; RADIAL DISTRIBUTION FUNCTION;

BIOCATALYSIS; CATALYTIC DOMAIN; DATABASES, PROTEIN; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE ANNOTATION; MUTATION; NONLINEAR DYNAMICS; OXIDOREDUCTASES; PHYSICOCHEMICAL PHENOMENA; SEQUENCE ALIGNMENT; TRANSFERASES;

EID: 84862157097     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-12-5     Document Type: Article

References (44)

1. The Protein Data Bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 1 235 242 10.1093/nar/28.1.235 10592235
2. Application of the three-dimensional structures of protein target molecules in structure-based drug design. Greer J, Erickson JW, Baldwin JJ, Varney MD, J Med Chem 1994 37 8 1035 1054 10.1021/jm00034a001 8164249
3. Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LP, J Bacteriol 2001 183 8 2405 2410 10.1128/JB.183.8.2405-2410.2001 11274097
4. Definitions of enzyme function for the structural genomics era. Babbitt PC, Curr Opin Chem Biol 2003 7 2 230 237 10.1016/S1367-5931(03)00028-0 12714057
5. Predicting protein function from sequence and structural data. Watson JD, Laskowski RA, Thornton JM, Curr Opin Struct Biol 2005 15 3 275 284 10.1016/j.sbi.2005.04.003 15963890
6. Flavoenzymes: diverse catalysts with recurrent features. Fraaije MW, Mattevi A, Trends in biochemical sciences 2000 25 3 126 132 10.1016/S0968- 0004(99)01533-9 10694883
7. Analysis of catalytic residues in enzyme active sites. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM, J Mol Biol 2002 324 1 105 121 10.1016/S0022-2836(02)01036-7 12421562
8. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Stark A, Russell RB, Nucleic Acids Res 2003 31 13 3341 3344 10.1093/nar/gkg506 12824322
9. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O, BMC bioinformatics 2008 9 17 10.1186/1471-2105-9-17 18190718
10. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O, Bioinformatics 2009 25 11 1426 1427 10.1093/bioinformatics/btp160 19307237
11. Evolutionary trace annotation of protein function in the structural proteome. Erdin S, Ward RM, Venner E, Lichtarge O, J Mol Biol 2010 396 5 1451 1473 10.1016/j.jmb.2009.12.037 20036248
12. FLORA: a novel method to predict protein function from structure in diverse superfamilies. Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA, PLoS computational biology 2009 5 8 1000485 10.1371/journal.pcbi.1000485 19714201
13. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Wallace AC, Borkakoti N, Thornton JM, Protein Sci 1997 6 11 2308 2323 9385633
14. Molecular shape comparisons in searches for active sites and functional similarity. Rosen M, Lin SL, Wolfson H, Nussinov R, Protein Eng 1998 11 4 263 277 10.1093/protein/11.4.263 9680188
15. Efficient similarity search in protein structure databases by k-clique hashing. Weskamp N, Kuhn D, Hullermeier E, Klebe G, Bioinformatics 2004 20 10 1522 1526 10.1093/bioinformatics/bth113 15231546
16. Recognition of functional sites in protein structures. Shulman-Peleg A, Nussinov R, Wolfson HJ, J Mol Biol 2004 339 3 607 633 10.1016/j.jmb.2004.04.012 15147845
17. A new method to detect related function among proteins independent of sequence and fold homology. Schmitt S, Kuhn D, Klebe G, J Mol Biol 2002 323 2 387 406 10.1016/S0022-2836(02)00811-2 12381328
18. Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network. Stahl M, Taroni C, Schneider G, Protein Engineering 2000 13 2 83 88 10.1093/protein/13.2.83 10708646
19. Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity. Kupas K, Ultsch A, Klebe G, Proteins 2007 71 3 1288 1306 10.1002/prot.21823
20. A new bioinformatic approach to detect common 3D sites in protein structures. Jambon M, Imberty A, Deleage G, Geourjon C, Proteins 2003 52 2 137 145 10.1002/prot.10339 12833538
21. A simple and fuzzy method to align and compare druggable ligand-binding sites. Schalon C, Surgand JS, Kellenberger E, Rognan D, Proteins 2008 71 4 1755 1778 10.1002/prot.21858 18175308
22. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA, PLoS computational biology 2009 5 12 1000585 10.1371/journal.pcbi.1000585 19997483
23. Prediction of active site cleft using support vector machines. Sonavane S, Chakrabarti P, J Chem Inf Model 2010 50 12 2266 2273 10.1021/ci1002922 21080689
24. Structural analyses of a malate dehydrogenase with a variable active site. Bell JK, Yennawar HP, Wright SK, Thompson JR, Viola RE, Banaszak LJ, J Biol Chem 2001 276 33 31156 31162 10.1074/jbc.M100902200 11389141
25. X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis. Wang JM, Mauro M, Edwards SL, Oatley SJ, Fishel LA, Ashford VA, Xuong NH, Kraut J, Biochemistry 1990 29 31 7160 7173 10.1021/bi00483a003 2169873
26. Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate. Didierjean C, Corbier C, Fatih M, Favier F, Boschi-Muller S, Branlant G, Aubry A, J Biol Chem 2003 278 15 12968 12976 10.1074/jbc.M211040200 12569100
27. Structure and mechanism of interleukin-1 beta converting enzyme. Wilson KP, Black JA, Thomson JA, Kim EE, Griffith JP, Navia MA, Murcko MA, Chambers SP, Aldape RA, Raybuck SA, et al. Nature 1994 370 6487 270 275 10.1038/370270a0 8035875
28. Study of the properties of phosphorylating D-glyceraldehyde-3-phosphate dehydrogenase. Nagradova NK, Biochemistry (Mosc) 2001 66 10 1067 1076 10.1023/A:1012472627801
29. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. Kotera M, Okuno Y, Hattori M, Goto S, Kanehisa M, J Am Chem Soc 2004 126 50 16487 16498 10.1021/ja0466457 15600352
30. The structure and function of G-protein-coupled receptors. Rosenbaum DM, Rasmussen SG, Kobilka BK, Nature 2009 459 7245 356 363 10.1038/nature08144 19458711
31. Twilight zone of protein sequence alignments. Rost B, Protein Eng 1999 12 2 85 94 10.1093/protein/12.2.85 10195279
32. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. Nagano N, Orengo CA, Thornton JM, J Mol Biol 2002 321 5 741 765 10.1016/S0022-2836(02) 00649-6 12206759
33. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM, Trends in biochemical sciences 1997 22 12 488 490 10.1016/S0968-0004(97)01140-7 9433130
34. Knowledge discovery in reaction databases: Landscaping organic reactions by a self-organizing neural network. Chen LR, Gasteiger J, J Am Chem Soc 1997 119 17 4033 4042 10.1021/ja960027b
35. Empirical Methods for the Calculation of Physicochemical Data of Organic Compounds. Gasteiger J, In: Physical Property Prediction in Organic Chemistry Springer, Heidelberg, Germany, Jochum C, Hicks MG, Sunkel J, 1988 119 138
36. PETRA server. http://www2.ccc.uni-erlangen.de/services/petra/
37. Prediction of H-1 NMR chemical shifts using neural networks. Aires-de-Sousa J, Hemmer MC, Gasteiger J, Anal Chem 2002 74 1 80 90 10.1021/ac010737m 11795822
38. Kohonen T, Self-organizing maps Springer, Berlin 3 2001
39. Identification of common molecular subsequences. Smith TF, Waterman MS, J Mol Biol 1981 147 1 195 197 10.1016/0022-2836(81)90087-5 7265238
40. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Needleman SB, Wunsch CD, J Mol Biol 1970 48 3 443 453 10.1016/0022-2836(70)90057-4 5420325
41. EMBOSS: the European Molecular Biology Open Software Suite. Rice P, Longden I, Bleasby A, Trends Genet 2000 16 6 276 277 10.1016/S0168-9525(00) 02024-2 10827456
42. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Ortiz AR, Strauss CE, Olmea O, Protein Sci 2002 11 11 2606 2621 12381844
43. An empirical Bayes approach to inferring large-scale gene association networks. Schafer J, Strimmer K, Bioinformatics 2005 21 6 754 764 10.1093/bioinformatics/bti062 15479708
44. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin AG, Brenner SE, Hubbard T, Chothia C, J Mol Biol 1995 247 4 536 540 7723011