A method to search for similar protein local structures at ligand- binding sites and its application to adenine recognition

European Biophysics Journal

Volumn 26, Issue 2, 1997, Pages 135-144

  Kobayashi, Nobuo ^a   Go, Nobuhiro ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Adenine recognition; Database search; Molecular recognition; Search for similar arrangements of atoms

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; ENZYME SPECIFICITY; LIGAND BINDING; MOLECULAR INTERACTION; PROTEIN STRUCTURE;

ADENINE; ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; CYCLIC AMP-DEPENDENT PROTEIN KINASES; DATABASES, FACTUAL; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEINS;

EID: 0030826293     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050065     Document Type: Article

References (43)

1. Artymiuk PJ, Poirrette AR, Rice DW, Willett P (1996) Biotin carboxylase comes into the fold. Nature Struct Biol 3:128-132
2. Belrhali H, Yaremchuk A, Tukalo M, Larsen K, Berthet-Colominas C, Leberman R, Beijer B, Sproat B, Als-Nielsen J, Grubel G, Legrand JF, Lehmann M, Cusack S (1994) Crystal structures at 2.5 À resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science 263:1432-1436
3. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The Protein Data Bank: a computer based archival file for macromolecular structures. J Mol Biol 122:535-542
4. 2+ adenylyl imidodiphosphate and inhibitor peptide PKI (5-24). EMBO J 12:849-859
5. Brady L, Brzozowski AM, Derewenda ZS, Dodson E, Dodson G, Tolley S, Turkenburg JP, Christiansen L, Huge-Jensen B, Norskov L (1990) A serine protease triad forms the catalytic centre of a triacylglycerol lipase. Nature 343:767-770
6. Coxeter HSM (1961) Introduction to Geometry. Wiley, New York
7. Dever TE, Glynias MJ, Merrick WC (1987) GTP-binding domain: three consensus sequence elements with distinct spacing. Proc Natl Acad Sci USA 84:1814-1818
8. Fan C, Moews PC, Shi Y, Walsh CT, Knox JR (1995) A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:D-alanine ligase of Escherichia coli. Proc Natl Acad Sci USA 92:1172-1176
9. Fan C, Moews PC, Walsh CT, Knox JR (1994) Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 Å resolution. Science 266:439-443
10. Finney JL (1975) Volume occupation, environment, and accessibility in proteins. The problem of the protein surface. J Mol Biol 96:721-732
11. Flaherty KM, McKay DB, Kabsch W, Holmes KC (1991) Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc Natl Acad Sci USA 88:5041-5045
12. Hanks SK, Quinn AM, Hunter T (1988) The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241:42-52
13. Hara T, Kato H, Katsube Y, Oda J (1996) A pseudo-Michaelis quaternary complex in the reverse reaction of a ligase; structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione and sulfate at 2.0-Å resolution. Biochemistry (in press)
14. Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ, Dunaway-Mariano D (1996) Swiveling-domina mechanism for enzymatic phosphotransfer between remote reaction sites. Proc Natl Acad Sci USA 93:2652-2657
15. Hibi T, Nishioka T, Kato H, Tanizawa K, Fukui T, Katsube Y, Oda J (1996) Structure of the multifunctional loops in the nonclassical ATP-binding fold of glutathione synthetase. Nature Struct Biol 3:16-18
16. Hubbard SR, Wei L, Ellis L, Hendrickson WA (1994) Crystal structure of the tyrosine kinase domain of the human insulin receptor. Nature 372:746-754
17. Glc with glycerol kinase. Science 259:673-677
18. Kobayashi N, Go N (1996a) ATP binding proteins with different folds share a common ATP-binding structural motif. Nature Struct Biol (in press)
19. Kobayashi N, Go N (1996b) Mechanical property of a TIM-barrel protein. Proteins (in press)
20. Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950
21. Matsuda K, Mizuguchi K, Nishioka T, Kato H, Go N, Oda J (1996) Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins. Protein Engineering (in press)
22. Moras D (1992) Structural and functional relationships between aminoacyl-tRNA synthetase. Trends Biochem Sci 17:159-164
23. Murzin AG (1996) Structural classification of proteins: new super-families. Curr Opin Struct Biol 6:386-394
24. Pearl L (1993) Similarity of active-site structures. Nature 362:24
25. Pearl L, Blundell T (1984) The active site of aspartic proteinases. FEBS Lett 174:96-101
26. Richards FM (1974) The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 82:1-14
27. Richards FM (1977) Areas, volumes, packing, and protein structure. Ann Rev Biophys Bioeng 6:151-176
28. Rould MA, Perona JJ, Steitz TA (1991) Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352:213-218
29. Schulz GE (1992) Binding of nucleotides by proteins. Curr Opin Struct Biol 2:61-67
30. Schulz GE, Schiltz E, Tomasselli AG, Frank R, Brune M, Wittinghofer A, Schirmer RH (1986) Structural relationships in the adenylate kinase family. Eur J Biochem 161:127-132
31. Story RM, Steitz TA (1992) Structure of the recA protein-ADP complex. Nature 355:374-376
32. Strynadka NC, Adachi H, Jensen SE, Johns K, Sielecki A, Betzel C, Sutoh K, James MN (1992) Molecular structure of the acylenzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution. Nature 359:700-705
33. Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, Toker L, Silman I (1991) Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Science 253:872-879
34. Swindells MG, Alexandrov NN (1994) Nucleotide binding in βαβ-βαβ topologies. Nature Struct Biol 1:677-678
35. Tanaka T, Kato H, Nishioka T, Oda J (1992) Mutational and proteolytic studies on a flexible loop in glutathione synthetase from Escherichia coli B: the loop and arginine 233 are critical for the catalytic reaction. Biochemistry 31:2259-2265
36. Tanaka T, Yamaguchi H, Kato H, Nishioka T, Katsube Y, Oda J (1993) Flexibility impaired by mutations revealed the multifunctional roles of the loop in glutathione synthetase. Biochemistry 32: 12398-12404
37. Tanemura M, Ogawa T, Ogita N (1983) A new algorithm for three-dimensional Voronoi tessellation. J Comp Phys 51:191-207
38. Traut TW (1994) The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur J Biochem 222:9-19
39. Waldrop GL, Rayment I, Holden HM (1994) Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry 33:10249-10256
40. Williams RL, Oren DA, Munoz-Dorado J, Inouye S, Inouye M, Arnold E (1993) Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 Å resolution. J Mol Biol 234:1230-1247
41. Wolodko WT, Fraser ME, James MN, Bridger WA (1994) The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-Å resolution. J Biol Chem 269:10883-10890
42. Xu RM, Carmel G, Sweet RM, Kuret J, Cheng X (1995) Crystal structure of casein kinase-1, a phosphate-directed protein kinase EMBO J 14:1015-1023
43. Yamaguchi H, Kato H, Hara Y, Nishioka T, Kumura A, Oda J, Katsube Y (1993) Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 Å resolution. J Mol Biol 229:1083-1100