메뉴 건너뛰기




Volumn 45, Issue 8, 2006, Pages 2545-2555

Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; ENZYMES; GENES; GENETIC ENGINEERING;

EID: 33644560639     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052101l     Document Type: Article
Times cited : (141)

References (61)
  • 1
    • 19344377263 scopus 로고    scopus 로고
    • Identifying protein function-a call for community action
    • Roberts, R. J. (2004) Identifying protein function-a call for community action, PLoS Biol. 2, E42.
    • (2004) PLoS Biol. , vol.2
    • Roberts, R.J.1
  • 2
    • 0001260894 scopus 로고
    • On the evolution of biochemical syntheses
    • Horowitz, N. H. (1945) On the evolution of biochemical syntheses, Proc. Natl. Acad. Sci. U.S.A. 31, 153-157.
    • (1945) Proc. Natl. Acad. Sci. U.S.A. , vol.31 , pp. 153-157
    • Horowitz, N.H.1
  • 3
    • 0001851565 scopus 로고
    • (Bryson, V., and Vogel, H. J., Eds.), Academic Press, New York
    • Horowitz, N. H. (1965) in Evolving Genes and Proteins (Bryson, V., and Vogel, H. J., Eds.) pp 15-, Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 15
    • Horowitz, N.H.1
  • 4
    • 0342276613 scopus 로고
    • The tryptophan synthase multienzyme complex: Exploring structure-function relationships with X-ray crystallography and mutagenesis
    • Hyde, C. C., and Miles, E. W. (1990) The tryptophan synthase multienzyme complex: exploring structure-function relationships with X-ray crystallography and mutagenesis, Biotechnology 8, 27-32.
    • (1990) Biotechnology , vol.8 , pp. 27-32
    • Hyde, C.C.1    Miles, E.W.2
  • 5
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen, R. A. (1976) Enzyme recruitment in evolution of new function, Annu. Rev. Microbiol. 30, 409-25.
    • (1976) Annu. Rev. Microbiol. , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 6
    • 0030667789 scopus 로고    scopus 로고
    • Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities
    • Babbitt, P. C., and Gerlt, J. A. (1997) Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities, J. Biol. Chem. 272, 30591-30594.
    • (1997) J. Biol. Chem. , vol.272 , pp. 30591-30594
    • Babbitt, P.C.1    Gerlt, J.A.2
  • 7
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt, J. A., and Babbitt, P. C. (2001) Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies, Annu. Rev. Biochem. 70, 209-246.
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 9
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd, A. E., Orengo, C. A., and Thornton, J. M. (2001) Evolution of function in protein superfamilies, from a structural perspective, J. Mol. Biol. 307, 1113-43.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 10
    • 0036306663 scopus 로고    scopus 로고
    • Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli
    • Rison, S. C., Teichmann, S. A., and Thornton, J. M. (2002) Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli, J. Mol. Biol. 318, 911-32.
    • (2002) J. Mol. Biol. , vol.318 , pp. 911-932
    • Rison, S.C.1    Teichmann, S.A.2    Thornton, J.M.3
  • 11
    • 0036303685 scopus 로고    scopus 로고
    • Evolution of enzymes in metabolism: A network perspective
    • Alves, R., Chaleil, R. A., and Sternberg, M. J. (2002) Evolution of enzymes in metabolism: a network perspective, J. Mol. Biol. 320, 751-70.
    • (2002) J. Mol. Biol. , vol.320 , pp. 751-770
    • Alves, R.1    Chaleil, R.A.2    Sternberg, M.J.3
  • 12
    • 0035943351 scopus 로고    scopus 로고
    • The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
    • Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., and Chothia, C. (2001) The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311, 693-708.
    • (2001) J. Mol. Biol. , vol.311 , pp. 693-708
    • Teichmann, S.A.1    Rison, S.C.2    Thornton, J.M.3    Riley, M.4    Gough, J.5    Chothia, C.6
  • 14
    • 9744279773 scopus 로고    scopus 로고
    • Divergent evolution in the enolase superfamily: The interplay of mechanism and specificity
    • Gerlt, J. A., Babbitt, P. C., and Rayment, I. (2005) Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity, Arch. Biochem. Biophys. 433, 59-70.
    • (2005) Arch. Biochem. Biophys. , vol.433 , pp. 59-70
    • Gerlt, J.A.1    Babbitt, P.C.2    Rayment, I.3
  • 15
    • 84984752764 scopus 로고    scopus 로고
    • Assignment of protein function in the postgenomic era
    • Saghatelian, A., and Cravatt, B. (2005) Assignment of protein function in the postgenomic era, Nat. Chem. Biol. 1, 130-142.
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 130-142
    • Saghatelian, A.1    Cravatt, B.2
  • 16
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough, J., Karplus, K., Hughey, R., and Chothia, C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure, J. Mol. Biol. 313, 903-919.
    • (2001) J. Mol. Biol. , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 18
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S. R. (1998) Profile hidden Markov models, Bioinformatics 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 19
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol. 247, 536-40.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 26
    • 0027665850 scopus 로고
    • Enzyme nomenclature: A personal retrospective
    • Webb, E. C. (1993) Enzyme nomenclature: a personal retrospective, FASEB J. 7, 1192-1194.
    • (1993) FASEB J. , vol.7 , pp. 1192-1194
    • Webb, E.C.1
  • 27
    • 0032168569 scopus 로고    scopus 로고
    • Catalytic triads and their relatives
    • Dodson, G., and Wlodawer, A. (1998) Catalytic triads and their relatives, Trends Biochem. Sci. 23, 347-352.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 347-352
    • Dodson, G.1    Wlodawer, A.2
  • 28
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter, C. T., Bartlett, G. J., and Thornton, J. M. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data, Nucleic Acids Res. 32, D129-133.
    • (2004) Nucleic Acids Res. , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 30
    • 13444302754 scopus 로고    scopus 로고
    • EzCatDB: The Enzyme Catalytic-mechanism Database
    • Nagano, N. (2005) EzCatDB: the Enzyme Catalytic-mechanism Database, Nucleic Acids Res. 33, D407-412.
    • (2005) Nucleic Acids Res. , vol.33
    • Nagano, N.1
  • 32
    • 15944418238 scopus 로고    scopus 로고
    • Representing structure-function relationships in mechanistically diverse enzyme superfamilies
    • Pegg, S. C., Brown, S., Ojha, S., Huang, C. C., Ferrin, T. E., and Babbitt, P. C. (2005) Representing structure-function relationships in mechanistically diverse enzyme superfamilies, Pac. Symp. Biocomput. 2005, 358-369.
    • (2005) Pac. Symp. Biocomput. , vol.2005 , pp. 358-369
    • Pegg, S.C.1    Brown, S.2    Ojha, S.3    Huang, C.C.4    Ferrin, T.E.5    Babbitt, P.C.6
  • 33
    • 0037780207 scopus 로고    scopus 로고
    • Evolutionary potential of (beta/alpha)8-barrels: Functional promiscuity produced by single substitutions in the enolase superfamily
    • Schmidt, D. M., Mundorff, E. C., Dojka, M., Bermudez, E., Ness, J. E., Govindarajan, S., Babbitt, P. C., Minshull, J., and Gerlt, J. A. (2003) Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily, Biochemistry 42, 8387-8393.
    • (2003) Biochemistry , vol.42 , pp. 8387-8393
    • Schmidt, D.M.1    Mundorff, E.C.2    Dojka, M.3    Bermudez, E.4    Ness, J.E.5    Govindarajan, S.6    Babbitt, P.C.7    Minshull, J.8    Gerlt, J.A.9
  • 34
    • 33745027619 scopus 로고    scopus 로고
    • The gold standard set of mechanistically diverse enzyme superfamilies
    • in press
    • Brown, S., Gerlt, J. A., Seffernick, J., and Babbitt, P. C., in press. The gold standard set of mechanistically diverse enzyme superfamilies, GenomeBiology.
    • GenomeBiology
    • Brown, S.1    Gerlt, J.A.2    Seffernick, J.3    Babbitt, P.C.4
  • 35
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos, D., and Valencia, A. (2001) Intrinsic errors in genome annotation, Trends Genet. 17, 429-431.
    • (2001) Trends Genet. , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 36
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner, S. E. (1999) Errors in genome annotation, Trends Genet 15, 132-133.
    • (1999) Trends Genet , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 41
    • 0035663042 scopus 로고    scopus 로고
    • Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase
    • Kurimoto, K., Fukai, S., Nureki, Ë., Muto, Y., and Yokoyama, S. (2001) Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase, Structure (Cambridge, MA, U.S.) 9, 1253-1263.
    • (2001) Structure (Cambridge, MA, U.S.) , vol.9 , pp. 1253-1263
    • Kurimoto, K.1    Fukai, S.2    Nureki, Ë.3    Muto, Y.4    Yokoyama, S.5
  • 42
    • 0035219809 scopus 로고    scopus 로고
    • Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): A perspective on enzymatic mechanisms
    • Meganathan, R. (2001) Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms, Vitam. Horm. 61, 173-218.
    • (2001) Vitam. Horm. , vol.61 , pp. 173-218
    • Meganathan, R.1
  • 45
    • 0033564297 scopus 로고    scopus 로고
    • Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723
    • Xu, L., Resing, K., Lawson, S. L., Babbitt, P. C., and Copley, S. D. (1999) Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723, Biochemistry 38, 7659-7669.
    • (1999) Biochemistry , vol.38 , pp. 7659-7669
    • Xu, L.1    Resing, K.2    Lawson, S.L.3    Babbitt, P.C.4    Copley, S.D.5
  • 46
    • 0035167572 scopus 로고    scopus 로고
    • A fully automatic evolutionary classification of protein folds: Dali domain dictionary version 3
    • Dietmann, S., Park, J., Notredame, C., Heger, A., Lappe, M., and Holm, L. (2001) A fully automatic evolutionary classification of protein folds: Dali domain dictionary version 3, Nucleic Acids Res. 29, 55-57.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 55-57
    • Dietmann, S.1    Park, J.2    Notredame, C.3    Heger, A.4    Lappe, M.5    Holm, L.6
  • 47
    • 0033556265 scopus 로고    scopus 로고
    • An archetypical extradiol-cleaving catecholic dioxygenase: The crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2
    • Kita, A., Kita, S., Fujisawa, L., Inaka, K., Ishida, T., Horiike, K., Nozaki, M., and Miki, K. (1999) An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2, Structure Fold Des. 7, 25-34.
    • (1999) Structure Fold Des. , vol.7 , pp. 25-34
    • Kita, A.1    Kita, S.2    Fujisawa, L.3    Inaka, K.4    Ishida, T.5    Horiike, K.6    Nozaki, M.7    Miki, K.8
  • 48
    • 0034649338 scopus 로고    scopus 로고
    • Mechanistic diversity in a metalloenzyme superfamily
    • Armstrong, R. N. (2000) Mechanistic diversity in a metalloenzyme superfamily, Biochemistry 39, 13625-13632.
    • (2000) Biochemistry , vol.39 , pp. 13625-13632
    • Armstrong, R.N.1
  • 49
    • 0032463747 scopus 로고    scopus 로고
    • All in the family: Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly
    • Bergdoll, M., Eltis, L. D., Cameron, A. D., Dumas, P., and Bolin, J. T. (1998) All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly, Protein Sci. 7, 1661 -1670.
    • (1998) Protein Sci. , vol.7 , pp. 1661-1670
    • Bergdoll, M.1    Eltis, L.D.2    Cameron, A.D.3    Dumas, P.4    Bolin, J.T.5
  • 50
  • 51
    • 0028116826 scopus 로고
    • Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search
    • Koonin, E. V., and Tatusov, R. L. (1994) Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search, J. Mol. Biol. 244, 125-132.
    • (1994) J. Mol. Biol. , vol.244 , pp. 125-132
    • Koonin, E.V.1    Tatusov, R.L.2
  • 52
    • 4344585269 scopus 로고    scopus 로고
    • Phosphoryl group transfer: Evolution of a catalytic scaffold
    • Allen, K. N., and Dunaway-Mariano, D. (2004) Phosphoryl group transfer: evolution of a catalytic scaffold, Trends Biochem. Sci. 29, 495-503.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 495-503
    • Allen, K.N.1    Dunaway-Mariano, D.2
  • 53
    • 0037176907 scopus 로고    scopus 로고
    • Structural mechanism of enoyl-CoA hydratase: Three atoms from a single water are added in either an Elcb stepwise or concerted fashion
    • Bahnson, B. J., Anderson, V. E., and Petsko, G. A. (2002) Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an Elcb stepwise or concerted fashion, Biochemistry 41, 2621-2629.
    • (2002) Biochemistry , vol.41 , pp. 2621-2629
    • Bahnson, B.J.1    Anderson, V.E.2    Petsko, G.A.3
  • 55
    • 0037560988 scopus 로고    scopus 로고
    • Mutagenesis approaches to deduce structure-function relationships in terpene synthases
    • Segura, M. J., Jackson, B. E., and Matsuda, S. P. (2003) Mutagenesis approaches to deduce structure-function relationships in terpene synthases, Nat. Prod. Rep. 20, 304-317.
    • (2003) Nat. Prod. Rep. , vol.20 , pp. 304-317
    • Segura, M.J.1    Jackson, B.E.2    Matsuda, S.P.3
  • 56
    • 17844384785 scopus 로고    scopus 로고
    • Structural and catalytic diversity within the amidohydrolase superfamily
    • Seibert, C. M., and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily, Biochemistry 44, 6383-6391.
    • (2005) Biochemistry , vol.44 , pp. 6383-6391
    • Seibert, C.M.1    Raushel, F.M.2
  • 60
    • 0023965741 scopus 로고
    • SMILES.1. Introduction and encoding rules
    • Weininger, D. J. (1988) SMILES.1. Introduction and encoding rules, J. Chem. Inf. Comput. Sci. 28, 31-46.
    • (1988) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-46
    • Weininger, D.J.1
  • 61
    • 0037397439 scopus 로고    scopus 로고
    • Definitions of enzyme function for the structural genomics era
    • Babbitt, P. C. (2003) Definitions of enzyme function for the structural genomics era, Curr. Opin. Chem. Biol. 7, 230-237.
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 230-237
    • Babbitt, P.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.