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Volumn 278, Issue 20, 2011, Pages 3835-3845

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

Author keywords

active sites; catalysis; enzyme; evolution; MACiE; mechanism; specificity; structure

Indexed keywords

AMINO ACID; CARBON MONOXIDE DEHYDROGENASE; CYTOCHROME C OXIDASE; GLUTAMINE FRUCTOSE 6 PHOSPHATE AMINOTRANSFERASE; HALOPEROXIDASE; METAL ION; PEROXIDASE; PROTEIN SERINE THREONINE KINASE; PYRUVATE DEHYDROGENASE; TRYPTASE; UNCLASSIFIED DRUG;

EID: 80053616941     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2011.08190.x     Document Type: Conference Paper
Times cited : (27)

References (44)
  • 1
    • 80053617193 scopus 로고    scopus 로고
    • ChEMBLDB. accessed 17 September 2010
    • ChEMBLDB., accessed 17 September 2010.
  • 4
    • 77957234003 scopus 로고    scopus 로고
    • The CoFactor database: Organic cofactors in enzyme catalysis
    • Fischer JD, Holliday GL, &, Thornton JM, (2010) The CoFactor database: organic cofactors in enzyme catalysis. Bioinformatics 26, 2496-2497.
    • (2010) Bioinformatics , vol.26 , pp. 2496-2497
    • Fischer, J.D.1    Holliday, G.L.2    Thornton, J.M.3
  • 8
    • 34249039579 scopus 로고    scopus 로고
    • The Geometry of Interactions between Catalytic Residues and their Substrates
    • DOI 10.1016/j.jmb.2007.03.055, PII S0022283607004093
    • Torrance JW, Holliday GL, Mitchell JBO, &, Thornton JM, (2007) The geometry of interactions between catalytic residues and their substrates. J Mol Biol 369, 1140-1152. (Pubitemid 46778698)
    • (2007) Journal of Molecular Biology , vol.369 , Issue.4 , pp. 1140-1152
    • Torrance, J.W.1    Holliday, G.L.2    Mitchell, J.B.O.3    Thornton, J.M.4
  • 10
    • 67549086082 scopus 로고    scopus 로고
    • Understanding the functional roles of amino acid residues in enzyme catalysis
    • Holliday GL, Mitchell JBO, &, Thornton JM, (2009) Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol 390, 560-577.
    • (2009) J Mol Biol , vol.390 , pp. 560-577
    • Holliday, G.L.1    Mitchell, J.B.O.2    Thornton, J.M.3
  • 11
    • 77949820602 scopus 로고    scopus 로고
    • Enzyme catalysis by hydrogen bonds: The balance between transition state binding and substrate binding in oxyanion holes
    • Simón L, &, Goodman JM, (2010) Enzyme catalysis by hydrogen bonds: the balance between transition state binding and substrate binding in oxyanion holes. J Org Chem 75, 1831-1840.
    • (2010) J Org Chem , vol.75 , pp. 1831-1840
    • Simón, L.1    Goodman, J.M.2
  • 12
    • 77950855514 scopus 로고    scopus 로고
    • Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: Implications for classification of enzyme function
    • Almonacid DE, Yera ER, Mitchell JBO, &, Babbitt PC, (2010) Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol 6, e1000700.
    • (2010) PLoS Comput Biol , vol.6
    • Almonacid, D.E.1    Yera, E.R.2    Mitchell, J.B.O.3    Babbitt, P.C.4
  • 13
    • 77958511659 scopus 로고    scopus 로고
    • The structures and physicochemical properties of organic cofactors in biocatalysis
    • Fischer JD, Holliday GL, Rahman SA, &, Thornton JM, (2010) The structures and physicochemical properties of organic cofactors in biocatalysis. J Mol Biol 403, 803-824.
    • (2010) J Mol Biol , vol.403 , pp. 803-824
    • Fischer, J.D.1    Holliday, G.L.2    Rahman, S.A.3    Thornton, J.M.4
  • 15
    • 33846041078 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res 35, D193-D197.
    • (2007) Nucleic Acids Res , vol.35
  • 16
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • DOI 10.1038/nsb1203-980
    • Berman H, Henrick K, &, Nakamura H, (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10, 980. (Pubitemid 37500485)
    • (2003) Nature Structural Biology , vol.10 , Issue.12 , pp. 980
    • Berman, H.1    Henrick, K.2    Nakamura, H.3
  • 19
    • 0141506108 scopus 로고    scopus 로고
    • L/D Protein Ligand Database (PLD): Additional understanding of the nature and specificity of protein-ligand complexes
    • DOI 10.1093/bioinformatics/btg243
    • Puvanendrampillai D, &, Mitchell JBO, (2003) Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 19, 1856-1857. (Pubitemid 37220482)
    • (2003) Bioinformatics , vol.19 , Issue.14 , pp. 1856-1857
    • Puvanendrampillai, D.1    Mitchell, J.B.O.2
  • 25
    • 13444302754 scopus 로고    scopus 로고
    • EzCatDB: The Enzyme Catalytic-mechanism Database
    • DOI 10.1093/nar/gki080
    • Nagano N, (2005) EzCatDB: The Enzyme Catalytic-Mechanism Database. Nucleic Acids Res 33, D407-D412. (Pubitemid 40207905)
    • (2005) Nucleic Acids Research , vol.33 , Issue.DATABASE ISS.
    • Nagano, N.1
  • 26
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, &, Thornton JM, (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32, D129-D133. (Pubitemid 38081621)
    • (2004) Nucleic Acids Research , vol.32 , Issue.DATABASE ISS.
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 28
    • 68549113108 scopus 로고    scopus 로고
    • Metal-MACiE: A database of metal ions involved in biological catalysis
    • Andreini C, Bertini I, Holliday GL, &, Thornton JM, (2009) Metal-MACiE: a database of metal ions involved in biological catalysis. Bioinformatics 25, 2088-2089.
    • (2009) Bioinformatics , vol.25 , pp. 2088-2089
    • Andreini, C.1    Bertini, I.2    Holliday, G.L.3    Thornton, J.M.4
  • 29
    • 0033588375 scopus 로고    scopus 로고
    • Heterologous expression of the vanadium-containing chloroperoxidase from Curvulariainaequalis in Saccharomyces cerevisiae and site-directed mutagenesis of the active site residues His(496), Lys(353), Arg(360), and Arg(490)
    • Hemrika W, Renirie R, Macedo-Ribeiro S, Messerschmidt A, &, Wever R, (1999) Heterologous expression of the vanadium-containing chloroperoxidase from Curvulariainaequalis in Saccharomyces cerevisiae and site-directed mutagenesis of the active site residues His(496), Lys(353), Arg(360), and Arg(490). J Biol Chem 274, 23820-23827.
    • (1999) J Biol Chem , vol.274 , pp. 23820-23827
    • Hemrika, W.1    Renirie, R.2    MacEdo-Ribeiro, S.3    Messerschmidt, A.4    Wever, R.5
  • 31
    • 0030906620 scopus 로고    scopus 로고
    • Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvularia inaequalis by X-ray structures of the native and peroxide form
    • Messerschmidt A, Prade L, &, Wever R, (1997) Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvulariainaequalis by X-ray structures of the native and peroxide form. Biol Chem 378, 309-315. (Pubitemid 27230618)
    • (1997) Biological Chemistry , vol.378 , Issue.3-4 , pp. 309-315
    • Messerschmidt, A.1    Prade, L.2    Wever, R.3
  • 32
    • 22844442470 scopus 로고    scopus 로고
    • Vanadium (V) peroxocomplexes: Structure, chemistry and biological implications
    • DOI 10.1016/j.jinorgbio.2005.04.003, PII S0162013405001005
    • Bortolini O, &, Conte V, (2005) Vanadium (V) peroxocomplexes: structure, chemistry and biological implications. J Inorg Biochem 99, 1549-1557. (Pubitemid 41039914)
    • (2005) Journal of Inorganic Biochemistry , vol.99 , Issue.8 , pp. 1549-1557
    • Bortolini, O.1    Conte, V.2
  • 33
    • 0035114957 scopus 로고    scopus 로고
    • cam and chloroperoxidase
    • DOI 10.1016/S0162-0134(00)00175-6, PII S0162013400001756
    • Woggon WD, Wagenknecht HA, &, Claude C, (2001) Synthetic active site analogues of heme-thiolate proteins. Characterization and identification of intermediates of the catalytic cycles of cytochrome P450cam and chloroperoxidase. J Inorg Biochem 83, 289-300. (Pubitemid 32186414)
    • (2001) Journal of Inorganic Biochemistry , vol.83 , Issue.4 , pp. 289-300
    • Woggon, W.-D.1    Wagenknecht, H.-A.2    Claude, C.3
  • 34
    • 0031149926 scopus 로고    scopus 로고
    • Identification of intermediates in the catalytic cycle of chloroperoxidase
    • Wagenknecht HA, &, Woggon WD, (1997) Identification of intermediates in the catalytic cycle of chloroperoxidase. Chem Biol 4, 367-372.
    • (1997) Chem Biol , vol.4 , pp. 367-372
    • Wagenknecht, H.A.1    Woggon, W.D.2
  • 35
    • 0032170496 scopus 로고    scopus 로고
    • Stereochemistry of the chloroperoxidase active site: Crystallographic and molecular-modeling studies
    • Sundaramoorthy M, Terner J, &, Poulos TL, (1998) Stereochemistry of the chloroperoxidase active site: crystallographic and molecular-modeling studies. Chem Biol 5, 461-473. (Pubitemid 28436725)
    • (1998) Chemistry and Biology , vol.5 , Issue.9 , pp. 461-473
    • Sundaramoorthy, M.1    Terner, J.2    Poulos, T.L.3
  • 37
    • 45849095719 scopus 로고    scopus 로고
    • How much of protein sequence space has been explored by life on Earth?
    • Dryden DTF, Thomson AR, &, White JH, (2008) How much of protein sequence space has been explored by life on Earth? J R Soc Interface 5, 953-995.
    • (2008) J R Soc Interface , vol.5 , pp. 953-995
    • Dryden, D.T.F.1    Thomson, A.R.2    White, J.H.3
  • 38
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, &, Sander C, (1996) Mapping the protein universe. Science 273, 595-602. (Pubitemid 26262103)
    • (1996) Science , vol.273 , Issue.5275 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 41
    • 50949084090 scopus 로고    scopus 로고
    • Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies
    • Chiang RA, Sali A, &, Babbitt PC, (2008) Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4, e1000142.
    • (2008) PLoS Comput Biol , vol.4
    • Chiang, R.A.1    Sali, A.2    Babbitt, P.C.3
  • 42
    • 0031666414 scopus 로고    scopus 로고
    • Analogous enzymes: Independent inventions in enzyme evolution
    • Galperin MY, Walker DR, &, Koonin EV, (1998) Analogous enzymes: independent inventions in enzyme evolution. Genome Res 8, 779-790. (Pubitemid 28458280)
    • (1998) Genome Research , vol.8 , Issue.8 , pp. 779-790
    • Galperin, M.Y.1    Walker, D.R.2    Koonin, E.V.3
  • 43
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14, 755-763. (Pubitemid 28552108)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 755-763
    • Eddy, S.R.1
  • 44
    • 58149187899 scopus 로고    scopus 로고
    • The CATH classification revisited - Architectures reviewed and new ways to characterize structural divergence in superfamilies
    • Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton JM, &, Orengo CA, (2009) The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res 37, D310-D314.
    • (2009) Nucleic Acids Res , vol.37
    • Cuff, A.L.1    Sillitoe, I.2    Lewis, T.3    Redfern, O.C.4    Garratt, R.5    Thornton, J.M.6    Orengo, C.A.7


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