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Volumn 51, Issue 1, 2003, Pages 96-108

Efficient identification of side-chain patterns using a multidimensional index tree

Author keywords

Function from structure; Functional site; Luciferase; Mirror image; SR tree; Structural bioinformatics

Indexed keywords

LUCIFERASE;

EID: 0037375799     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10338     Document Type: Article
Times cited : (29)

References (48)
  • 1
    • 0035367880 scopus 로고    scopus 로고
    • Determination of protein function, evolution and interactions by structural genomics
    • Teichmann SA, Murzin AG, Chothia C. Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol 2001;11:354-363.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 354-363
    • Teichmann, S.A.1    Murzin, A.G.2    Chothia, C.3
  • 3
    • 0035367071 scopus 로고    scopus 로고
    • Protein structure similarities
    • Koehl P. Protein structure similarities. Curr Opin Struct Biol 2001;11:348-353.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 348-353
    • Koehl, P.1
  • 4
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • 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;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 5
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
    • (1997) Nucleic Acids Res , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 7
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous families
    • Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998;7:2469-2471.
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 8
    • 0035165967 scopus 로고    scopus 로고
    • A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
    • Shindyalov IN, Bourne PE. A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res 2001;29:228-229.
    • (2001) Nucleic Acids Res , vol.29 , pp. 228-229
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 9
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • Russell RB, Sasieni PD, Sternberg MJ. Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 1998;282:903-918.
    • (1998) J Mol Biol , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 10
    • 0027967593 scopus 로고
    • A graphtheoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
    • Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW, Willett P. A graphtheoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol 1994;243:327-344.
    • (1994) J Mol Biol , vol.243 , pp. 327-344
    • Artymiuk, P.J.1    Poirrette, A.R.2    Grindley, H.M.3    Rice, D.W.4    Willett, P.5
  • 11
    • 0030724039 scopus 로고    scopus 로고
    • 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. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6:2308-2323.
    • (1997) Protein Sci , vol.6 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 12
    • 0032568859 scopus 로고    scopus 로고
    • Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution
    • Russell RB. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 1998;279:1211-1227.
    • (1998) J Mol Biol , vol.279 , pp. 1211-1227
    • Russell, R.B.1
  • 13
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial-motifs in protein structures
    • Kleywegt GJ. Recognition of spatial-motifs in protein structures. J Mol Biol 1999;285:1887-1897.
    • (1999) J Mol Biol , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 14
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases
    • Fetrow JS, Skolnick J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 1998;281:949-968.
    • (1998) J Mol Biol , vol.281 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 15
    • 0035861977 scopus 로고    scopus 로고
    • Recognition templates for predicting adenylate-binding sites in proteins
    • Zhao S, Morris GM, Olson AJ, Goodsell DS. Recognition templates for predicting adenylate-binding sites in proteins. J Mol Biol 2001;314:1245-1255.
    • (2001) J Mol Biol , vol.314 , pp. 1245-1255
    • Zhao, S.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 16
    • 0033582329 scopus 로고    scopus 로고
    • Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
    • Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci USA 1999;96:400-405.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 400-405
    • Lovell, S.C.1    Word, J.M.2    Richardson, J.S.3    Richardson, D.C.4
  • 17
  • 18
    • 0034599484 scopus 로고    scopus 로고
    • The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alphacarbonic anhydrases
    • Kimber MS, Pai EF. The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alphacarbonic anhydrases. EMBO J 2000;19:1407-1418.
    • (2000) EMBO J , vol.19 , pp. 1407-1418
    • Kimber, M.S.1    Pai, E.F.2
  • 19
    • 0034663814 scopus 로고    scopus 로고
    • The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site
    • Pawelek PD, Cheah J, Coulombe R, Macheroux P, Ghisla S, Vrielink A. The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site. EMBO J 2000;19:4204-4215.
    • (2000) EMBO J , vol.19 , pp. 4204-4215
    • Pawelek, P.D.1    Cheah, J.2    Coulombe, R.3    Macheroux, P.4    Ghisla, S.5    Vrielink, A.6
  • 20
    • 0035799315 scopus 로고    scopus 로고
    • Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis
    • Wood ZA, Poole LB, Karplus PA. Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis. Biochemistry 2001;40:3900-3911.
    • (2001) Biochemistry , vol.40 , pp. 3900-3911
    • Wood, Z.A.1    Poole, L.B.2    Karplus, P.A.3
  • 21
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991;24:946-950.
    • (1991) J Appl Cryst , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 22
    • 0031162081 scopus 로고    scopus 로고
    • The SR-tree: An index structure for high-dimensional nearest neighbor queries
    • Tucson, Arizona
    • Katayama N, Satoh S. The SR-tree: an index structure for high-dimensional nearest neighbor queries. Proceedings of ACM SIGMOD, Tucson, Arizona, 1997;May 13-15:369-380.
    • (1997) Proceedings of ACM SIGMOD , vol.MAY 13-15 , pp. 369-380
    • Katayama, N.1    Satoh, S.2
  • 23
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 2000;28:254-256.
    • (2000) Nucleic Acids Res , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 24
    • 0032168569 scopus 로고    scopus 로고
    • Catalytic triads and their relatives
    • Dodson G, Wlodawer A. Catalytic triads and their relatives. Trends Biochem Sci 1998;23:347-352.
    • (1998) Trends Biochem Sci , vol.23 , pp. 347-352
    • Dodson, G.1    Wlodawer, A.2
  • 25
    • 0026432669 scopus 로고
    • Ser-His-Glu triad:Forms the catalytic site of the lipase from Geotrichum candidum
    • Schrag JD, Li YG, Wu S, Cygler M. Ser-His-Glu triad:Forms the catalytic site of the lipase from Geotrichum candidum. Nature 1991;351:761-764.
    • (1991) Nature , vol.351 , pp. 761-764
    • Schrag, J.D.1    Li, Y.G.2    Wu, S.3    Cygler, M.4
  • 26
    • 0027972854 scopus 로고
    • Classification of serine proteases derived from steric comparisons of their active sites, part II: Ser, His, Asp arrangements in proteolytic and nonproteolytic proteins
    • Barth A, Frost K, Wahab M, Brandt W, Schadler HD, Franke R. Classification of serine proteases derived from steric comparisons of their active sites, part II: Ser, His, Asp arrangements in proteolytic and nonproteolytic proteins. Drug Des Discov 1994;12:89-111.
    • (1994) Drug Des Discov , vol.12 , pp. 89-111
    • Barth, A.1    Frost, K.2    Wahab, M.3    Brandt, W.4    Schadler, H.D.5    Franke, R.6
  • 27
    • 0023192209 scopus 로고
    • Rat submaxillary gland serine protease, tonin, Structure solution and refinement at 1.8 A resolution
    • Fujinaga M, James MN. Rat submaxillary gland serine protease, tonin, Structure solution and refinement at 1.8 A resolution. J Mol Biol 1987;195:373-396.
    • (1987) J Mol Biol , vol.195 , pp. 373-396
    • Fujinaga, M.1    James, M.N.2
  • 28
    • 0031574232 scopus 로고    scopus 로고
    • The 2-His-1-carboxylate facial triad-an emerging structural motif in mononuclear non-heme iron(II) enzymes
    • Hegg EL, Que L Jr. The 2-His-1-carboxylate facial triad-an emerging structural motif in mononuclear non-heme iron(II) enzymes. Eur J Biochem 1997;250:625-629.
    • (1997) Eur J Biochem , vol.250 , pp. 625-629
    • Hegg, E.L.1    Que L., Jr.2
  • 29
    • 0025906404 scopus 로고
    • Three-dimensional structure of the elastase of Pseudormonas aeruginosa at 1.5-Ä resolution
    • Thayer MM, Flaherty KM, McKay DB. Three-dimensional structure of the elastase of Pseudormonas aeruginosa at 1.5-Ä resolution. J Biol Chem 1991;266:2864-2871.
    • (1991) J Biol Chem , vol.266 , pp. 2864-2871
    • Thayer, M.M.1    Flaherty, K.M.2    McKay, D.B.3
  • 30
    • 0031010420 scopus 로고    scopus 로고
    • Crystal structure of tyrosine hydroxylase at 2.3 Ä and its implications for inherited neurodegenerative diseases
    • Goodwill KE, Sabatier C, Marks C, Raag R, Fitzpatrick PF, Stevens RC. Crystal structure of tyrosine hydroxylase at 2.3 Ä and its implications for inherited neurodegenerative diseases. Nat Struct Biol 1997;4:578-585.
    • (1997) Nat Struct Biol , vol.4 , pp. 578-585
    • Goodwill, K.E.1    Sabatier, C.2    Marks, C.3    Raag, R.4    Fitzpatrick, P.F.5    Stevens, R.C.6
  • 31
    • 0029664970 scopus 로고    scopus 로고
    • The 1.5-Ä resolution crystal structure of bacterial luciferase in low salt conditions
    • Fisher AJ, Thompson TB, Thoden JB, Baldwin TO, Rayment I. The 1.5-Ä resolution crystal structure of bacterial luciferase in low salt conditions. J Biol Chem 1996;271:21956-21968.
    • (1996) J Biol Chem , vol.271 , pp. 21956-21968
    • Fisher, A.J.1    Thompson, T.B.2    Thoden, J.B.3    Baldwin, T.O.4    Rayment, I.5
  • 32
    • 0034654852 scopus 로고    scopus 로고
    • The 1.8 Ä crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker
    • Vetting MW, Ohlendorf DH. The 1.8 Ä crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker. Structure Fold Des 2000;8:429-440.
    • (2000) Structure Fold Des , vol.8 , pp. 429-440
    • Vetting, M.W.1    Ohlendorf, D.H.2
  • 33
    • 0031047622 scopus 로고    scopus 로고
    • Structure of bacterial luciferase beta 2 homodimer: Implications for flavin binding
    • Tanner JJ, Miller MD, Wilson KS, Tu SC, Krause KL. Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding. Biochemistry 1997;36:665-672.
    • (1997) Biochemistry , vol.36 , pp. 665-672
    • Tanner, J.J.1    Miller, M.D.2    Wilson, K.S.3    Tu, S.C.4    Krause, K.L.5
  • 34
    • 0026071817 scopus 로고
    • Molecular biology of bacterial bioluminescence
    • Meighen EA. Molecular biology of bacterial bioluminescence. Microbiol Rev 1991;55:123-142.
    • (1991) Microbiol Rev , vol.55 , pp. 123-142
    • Meighen, E.A.1
  • 36
    • 0034802540 scopus 로고    scopus 로고
    • Enzyme mechanism and catalytic property of beta propeller phytase
    • Shin S, Ha NC, Oh BC, Oh TK, Oh BH. Enzyme mechanism and catalytic property of beta propeller phytase. Structure 2001;9:851-858.
    • (2001) Structure , vol.9 , pp. 851-858
    • Shin, S.1    Ha, N.C.2    Oh, B.C.3    Oh, T.K.4    Oh, B.H.5
  • 37
    • 0035859795 scopus 로고    scopus 로고
    • Calcium-dependent catalytic activity of a novel phytase from Bacillus amyloliquefaciens DS11
    • Oh BC, Chang BS, Park KH, Ha NC, Kim HK, Oh BH, Oh TK. Calcium-dependent catalytic activity of a novel phytase from Bacillus amyloliquefaciens DS11. Biochemistry 2001;40:9669-9676.
    • (2001) Biochemistry , vol.40 , pp. 9669-9676
    • Oh, B.C.1    Chang, B.S.2    Park, K.H.3    Ha, N.C.4    Kim, H.K.5    Oh, B.H.6    Oh, T.K.7
  • 38
    • 0035805603 scopus 로고    scopus 로고
    • Mechanistic inferences from the crystal structure of fumarylacetoacetate hydrolase with a bound phosphorus-based inhibitor
    • Bateman RL, Bhanumoorthy P, Witte JF, McClard RW, Grompe M, Timm DE. Mechanistic inferences from the crystal structure of fumarylacetoacetate hydrolase with a bound phosphorus-based inhibitor. J Biol Chem 2001;276:15284-15291.
    • (2001) J Biol Chem , vol.276 , pp. 15284-15291
    • Bateman, R.L.1    Bhanumoorthy, P.2    Witte, J.F.3    McClard, R.W.4    Grompe, M.5    Timm, D.E.6
  • 39
    • 0031567156 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus
    • Wallon G, Kryger G, Lovett ST, Oshima T, Ringe D, Petsko GA. Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J Mol Biol 1997;266:1016-1031.
    • (1997) J Mol Biol , vol.266 , pp. 1016-1031
    • Wallon, G.1    Kryger, G.2    Lovett, S.T.3    Oshima, T.4    Ringe, D.5    Petsko, G.A.6
  • 42
    • 0028952279 scopus 로고
    • Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli
    • Lee ME, Dyer DH, Klein OD, Bolduc JM, Stoddard BL, Koshland DE Jr. Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli. Biochemistry 1995;34:378-384.
    • (1995) Biochemistry , vol.34 , pp. 378-384
    • Lee, M.E.1    Dyer, D.H.2    Klein, O.D.3    Bolduc, J.M.4    Stoddard, B.L.5    Koshland D.E., Jr.6
  • 43
    • 0031877016 scopus 로고    scopus 로고
    • Combining evidence using p-values: Application to sequence homology searches
    • Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998;14:48-54.
    • (1998) Bioinformatics , vol.14 , pp. 48-54
    • Bailey, T.L.1    Gribskov, M.2
  • 44
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • Peters KP, Fauck J, Frommel C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol 1996;256:201-213.
    • (1996) J Mol Biol , vol.256 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frommel, C.3
  • 45
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock AH. Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol 2001;312:885-896.
    • (2001) J Mol Biol , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 46
    • 0035838976 scopus 로고    scopus 로고
    • Automated structurebased prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy P, Querol E, Aviles FX, Sternberg MJ. Automated structurebased prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 2001;311:395-408.
    • (2001) J Mol Biol , vol.311 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.4
  • 47
    • 0035853280 scopus 로고    scopus 로고
    • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    • 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.
    • (2001) J Mol Biol , vol.307 , pp. 1487-1502
    • Landgraf, R.1    Xenarios, I.2    Eisenberg, D.3
  • 48
    • 0037007068 scopus 로고    scopus 로고
    • Computational mapping identifies the binding sites of organic solvents on proteins
    • Dennis S, Kortvelyesi T, Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci USA 2002;99:4290-4295.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 4290-4295
    • Dennis, S.1    Kortvelyesi, T.2    Vajda, S.3


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