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Volumn 28, Issue 6, 2003, Pages 336-341

Metabolites: A helping hand for pathway evolution?

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

EID: 0038434059     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0968-0004(03)00114-2     Document Type: Review
Times cited : (117)

References (58)
  • 1
    • 0036303685 scopus 로고    scopus 로고
    • Evolution of enzymes in metabolism: A network perspective
    • Alves R., et al. Evolution of enzymes in metabolism: a network perspective. J. Mol. Biol. 320:2002;751-770.
    • (2002) J. Mol. Biol. , vol.320 , pp. 751-770
    • Alves, R.1
  • 2
    • 0035232163 scopus 로고    scopus 로고
    • An insight into domain combinations
    • Apic G., et al. An insight into domain combinations. Bioinformatics. 17:(Suppl. 1):2001;S83-S89.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Apic, G.1
  • 3
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • Apic G., et al. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:2001;311-325.
    • (2001) J. Mol. Biol. , vol.310 , pp. 311-325
    • Apic, G.1
  • 4
    • 0034601917 scopus 로고    scopus 로고
    • Homology among (βα)8-barrels: Implications for the evolution of metabolic pathways
    • Copley R.R., Bork P. Homology among (βα)8-barrels: implications for the evolution of metabolic pathways. J. Mol. Biol. 303:2000;627-641.
    • (2000) J. Mol. Biol. , vol.303 , pp. 627-641
    • Copley, R.R.1    Bork, P.2
  • 5
    • 0033597176 scopus 로고    scopus 로고
    • The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
    • Hegyi H., Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288:1999;147-164.
    • (1999) J. Mol. Biol. , vol.288 , pp. 147-164
    • Hegyi, H.1    Gerstein, M.2
  • 6
    • 0036016436 scopus 로고    scopus 로고
    • Structural basis for broad substrate specificity in higher plant β-D-glucan glucohydrolases
    • Hrmova M., et al. Structural basis for broad substrate specificity in higher plant β-D-glucan glucohydrolases. Plant Cell. 14:2002;1033-1052.
    • (2002) Plant Cell , vol.14 , pp. 1033-1052
    • Hrmova, M.1
  • 7
    • 0034883978 scopus 로고    scopus 로고
    • Divergence of function in sequence-related groups of Escherichia coli proteins
    • Nahum L.A., Riley M. Divergence of function in sequence-related groups of Escherichia coli proteins. Genome Res. 11:2001;1375-1381.
    • (2001) Genome Res. , vol.11 , pp. 1375-1381
    • Nahum, L.A.1    Riley, M.2
  • 8
    • 0036407027 scopus 로고    scopus 로고
    • Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: The replacement of the missing 'household' nucleoside diphosphate kinase gene and activity by glycolytic kinases
    • Pollack J.D., et al. Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing 'household' nucleoside diphosphate kinase gene and activity by glycolytic kinases. OMICS. 6:2002;247-258.
    • (2002) OMICS , vol.6 , pp. 247-258
    • Pollack, J.D.1
  • 9
    • 0036306663 scopus 로고    scopus 로고
    • Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli
    • Rison S.C.G., et al. Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J. Mol. Biol. 318:2002;911-932.
    • (2002) J. Mol. Biol. , vol.318 , pp. 911-932
    • Rison, S.C.G.1
  • 11
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318:2002;595-608.
    • (2002) J. Mol. Biol. , vol.318 , pp. 595-608
    • Rost, B.1
  • 12
    • 0035575588 scopus 로고    scopus 로고
    • Small-molecule metabolism: An enzyme mosaic
    • Teichmann S.A., et al. Small-molecule metabolism: an enzyme mosaic. Trends Biotechnol. 19:2001;482-486.
    • (2001) Trends Biotechnol. , vol.19 , pp. 482-486
    • Teichmann, S.A.1
  • 13
    • 0035943351 scopus 로고    scopus 로고
    • The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli
    • Teichmann S.A., et al. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311:2001;693-708.
    • (2001) J. Mol. Biol. , vol.311 , pp. 693-708
    • Teichmann, S.A.1
  • 14
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd A.E., et al. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1
  • 15
    • 0037022651 scopus 로고    scopus 로고
    • Transfer RNA-dependent amino acid biosynthesis: An essential route to asparagine formation
    • Min B., et al. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. U. S. A. 99:2002;2678-2683.
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 2678-2683
    • Min, B.1
  • 16
    • 0001260894 scopus 로고
    • On the evolution of biochemical syntheses
    • Horowitz N.H. On the evolution of biochemical syntheses. Proc. Natl. Acad. Sci. U. S. A. 31:1945;153-157.
    • (1945) Proc. Natl. Acad. Sci. U. S. A. , vol.31 , pp. 153-157
    • Horowitz, N.H.1
  • 17
    • 0001851565 scopus 로고
    • The evolution of biochemical syntheses - retrospect and prospect
    • V. Bryson, & J.H. Vogel. Academic Press
    • Horowitz N.H. The evolution of biochemical syntheses - retrospect and prospect. Bryson V., Vogel J.H. Evolving Genes and Proteins. 1965;15-23 Academic Press.
    • (1965) Evolving Genes and Proteins , pp. 15-23
    • Horowitz, N.H.1
  • 19
    • 0027487948 scopus 로고
    • On the origin of enzymatic species
    • Petsko G.A., et al. On the origin of enzymatic species. Trends Biochem. Sci. 18:1993;372-376.
    • (1993) Trends Biochem. Sci. , vol.18 , pp. 372-376
    • Petsko, G.A.1
  • 20
    • 0032738446 scopus 로고    scopus 로고
    • Multifunctional enzymes and evolution of biosynthetic pathways: Retro-evolution by jumps
    • Roy S. Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps. Proteins. 37:1999;303-309.
    • (1999) Proteins , vol.37 , pp. 303-309
    • Roy, S.1
  • 21
    • 0033117461 scopus 로고    scopus 로고
    • Catalytic promiscuity and the evolution of new enzymatic activities
    • O'Brien P.J., Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6:1999;R91-R105.
    • (1999) Chem. Biol. , vol.6
    • O'Brien, P.J.1    Herschlag, D.2
  • 23
    • 0033940941 scopus 로고    scopus 로고
    • Gene and context: Integrative approaches to genome analysis
    • Huynen M.A., Snel B. Gene and context: integrative approaches to genome analysis. Adv. Protein Chem. 54:2000;345-379.
    • (2000) Adv. Protein Chem. , vol.54 , pp. 345-379
    • Huynen, M.A.1    Snel, B.2
  • 24
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt J.A., Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70:2001;209-246.
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 25
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30:1976;409-425.
    • (1976) Annu. Rev. Microbiol. , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 26
    • 0002624741 scopus 로고    scopus 로고
    • Evolution of metabolic pathways in enteric bacteria
    • F.C. et al. Neidhardt. ASM Press
    • Jensen R.A. Evolution of metabolic pathways in enteric bacteria. Neidhardt F.C., et al. Escherichia coli and Salmonella. 1996;2649-2662 ASM Press.
    • (1996) Escherichia coli and Salmonella , pp. 2649-2662
    • Jensen, R.A.1
  • 27
    • 0015980083 scopus 로고
    • On earlier states of the biochemical system
    • Ycas M. On earlier states of the biochemical system. J. Theor. Biol. 44:1974;145-160.
    • (1974) J. Theor. Biol. , vol.44 , pp. 145-160
    • Ycas, M.1
  • 28
    • 0032527783 scopus 로고    scopus 로고
    • Protein folds and functions
    • Martin A.C., et al. Protein folds and functions. Structure. 6:1998;875-884.
    • (1998) Structure , vol.6 , pp. 875-884
    • Martin, A.C.1
  • 29
    • 0034739441 scopus 로고    scopus 로고
    • Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes
    • Nara T., et al. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene. 257:2000;209-222.
    • (2000) Gene , vol.257 , pp. 209-222
    • Nara, T.1
  • 30
    • 0034730195 scopus 로고    scopus 로고
    • Directed evolution of a (βα)8-barrel enzyme to catalyze related reactions in two different metabolic pathways
    • Jürgens C., et al. Directed evolution of a (βα)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc. Natl. Acad. Sci. U. S. A. 97:2000;9925-9930.
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 9925-9930
    • Jürgens, C.1
  • 31
    • 0030777303 scopus 로고    scopus 로고
    • CATH - A hierarchic classification of protein domain structures
    • Orengo C.A., et al. CATH - a hierarchic classification of protein domain structures. Structure. 5:1997;1093-1108.
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.A.1
  • 32
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1
  • 33
    • 0026687729 scopus 로고
    • An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins
    • Bork P., et al. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. U. S. A. 89:1992;7290-7294.
    • (1992) Proc. Natl. Acad. Sci. U. S. A. , vol.89 , pp. 7290-7294
    • Bork, P.1
  • 34
    • 0034033261 scopus 로고    scopus 로고
    • History of the enzyme nomenclature system
    • Tipton K., Boyce S. History of the enzyme nomenclature system. Bioinformatics. 16:2000;34-40.
    • (2000) Bioinformatics , vol.16 , pp. 34-40
    • Tipton, K.1    Boyce, S.2
  • 35
    • 0028470228 scopus 로고
    • Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB). enzyme nomenclature. Recommendations 1992. Supplement: Corrections and additions
    • Tipton K.F. Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB). enzyme nomenclature. Recommendations 1992. Supplement: corrections and additions. Eur. J. Biochem. 223:1994;1-5.
    • (1994) Eur. J. Biochem. , vol.223 , pp. 1-5
    • Tipton, K.F.1
  • 37
    • 0033571352 scopus 로고    scopus 로고
    • Glycyl radical enzymes: A conservative structural basis for radicals
    • Eklund H., Fontecave M. Glycyl radical enzymes: a conservative structural basis for radicals. Structure Fold. Des. 7:1999;R257-R262.
    • (1999) Structure Fold. Des. , vol.7
    • Eklund, H.1    Fontecave, M.2
  • 38
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • Lawrence J.G., Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:1997;383-397.
    • (1997) J. Mol. Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 39
  • 40
    • 0036081012 scopus 로고    scopus 로고
    • BRENDA, enzyme data and metabolic information
    • Schomburg I., et al. BRENDA, enzyme data and metabolic information. Nucleic Acids Res. 30:2002;47-49.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 47-49
    • Schomburg, I.1
  • 41
    • 0032005335 scopus 로고    scopus 로고
    • Underground metabolism
    • D'Ari R., Casadesús J. Underground metabolism. Bioessays. 20:1998;181-186.
    • (1998) Bioessays , vol.20 , pp. 181-186
    • D'Ari, R.1    Casadesús, J.2
  • 42
    • 0035798398 scopus 로고    scopus 로고
    • Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model
    • Qian J., et al. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J. Mol. Biol. 313:2001;673-681.
    • (2001) J. Mol. Biol. , vol.313 , pp. 673-681
    • Qian, J.1
  • 43
    • 0030963745 scopus 로고    scopus 로고
    • The exaptive excellence of spandrels as a term and prototype
    • Gould S.J. The exaptive excellence of spandrels as a term and prototype. Proc. Natl. Acad. Sci. U. S. A. 94:1997;10750-10755.
    • (1997) Proc. Natl. Acad. Sci. U. S. A. , vol.94 , pp. 10750-10755
    • Gould, S.J.1
  • 44
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong H., et al. The large-scale organization of metabolic networks. Nature. 407:2000;651-654.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1
  • 45
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • Strogatz S.H. Exploring complex networks. Nature. 410:2001;268-276.
    • (2001) Nature , vol.410 , pp. 268-276
    • Strogatz, S.H.1
  • 46
    • 0035823264 scopus 로고    scopus 로고
    • The small world inside large metabolic networks
    • Wagner A., Fell D.A. The small world inside large metabolic networks. Proc. R. Soc. Lond. B Biol. Sci. 268:2001;1803-1810.
    • (2001) Proc. R. Soc. Lond. B Biol. Sci. , vol.268 , pp. 1803-1810
    • Wagner, A.1    Fell, D.A.2
  • 47
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz E., et al. Hierarchical organization of modularity in metabolic networks. Science. 297:2002;1551-1555.
    • (2002) Science , vol.297 , pp. 1551-1555
    • Ravasz, E.1
  • 48
    • 0034213801 scopus 로고    scopus 로고
    • Evolution of a metabolic pathway for degradation of a toxic xenobiotic: The patchwork approach
    • Copley S.D. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem. Sci. 25:2000;261-265.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 261-265
    • Copley, S.D.1
  • 49
    • 0028020325 scopus 로고
    • Higher plant metabolism of xenobiotics: The 'green liver' concept
    • Sandermann H.J. Higher plant metabolism of xenobiotics: the 'green liver' concept. Pharmacogenetics. 4:1994;225-241.
    • (1994) Pharmacogenetics , vol.4 , pp. 225-241
    • Sandermann, H.J.1
  • 50
    • 0034876239 scopus 로고    scopus 로고
    • Comparable system-level organization of Archaea and Eukaryotes
    • Podani J., et al. Comparable system-level organization of Archaea and Eukaryotes. Nat. Genet. 29:2001;54-56.
    • (2001) Nat. Genet. , vol.29 , pp. 54-56
    • Podani, J.1
  • 51
    • 0036081062 scopus 로고    scopus 로고
    • The KEGG databases at GenomeNet
    • Kanehisa M., et al. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:2002;42-46.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 42-46
    • Kanehisa, M.1
  • 52
    • 0033721503 scopus 로고    scopus 로고
    • Graph structure in the web
    • Broder A., et al. Graph structure in the web. Comput. Netw. 33:2000;309-320.
    • (2000) Comput. Netw. , vol.33 , pp. 309-320
    • Broder, A.1
  • 53
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • Snel B., et al. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. U. S. A. 99:2002;5890-5895.
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 5890-5895
    • Snel, B.1
  • 54
    • 0036081122 scopus 로고    scopus 로고
    • LIGAND: Database of chemical compounds and reactions in biological pathways
    • Goto S., et al. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30:2002;402-404.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 402-404
    • Goto, S.1
  • 55
    • 0032176603 scopus 로고    scopus 로고
    • Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis
    • Gerlt J.A., Babbitt P.C. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Curr. Opin. Chem. Biol. 2:1998;607-612.
    • (1998) Curr. Opin. Chem. Biol. , vol.2 , pp. 607-612
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 56
    • 0033382609 scopus 로고    scopus 로고
    • Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes
    • Galperin M.Y., Koonin E.V. Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. Genetica. 106:1999;159-170.
    • (1999) Genetica , vol.106 , pp. 159-170
    • Galperin, M.Y.1    Koonin, E.V.2
  • 57
    • 0031666414 scopus 로고    scopus 로고
    • Analogous enzymes: Independent inventions in enzyme evolution
    • Galperin M.Y., et al. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8:1998;779-790.
    • (1998) Genome Res. , vol.8 , pp. 779-790
    • Galperin, M.Y.1
  • 58
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch A. The ENZYME database in 2000. Nucleic Acids Res. 28:2000;304-305.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 304-305
    • Bairoch, A.1


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