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Volumn 50, Issue 46, 2011, Pages 9950-9962

The enzyme function initiative

(15)  Gerlt, John A a   Allen, Karen N b   Almo, Steven C c   Armstrong, Richard N d   Babbitt, Patricia C e   Cronan, John E a   Dunaway Mariano, Debra f   Imker, Heidi J a   Jacobson, Matthew P g   Minor, Wladek h   Poulter, C Dale a   Raushel, Frank M i   Sali, Andrej j   Shoichet, Brian K g   Sweedler, Jonathan V a  


Author keywords

[No Author keywords available]

Indexed keywords

AMIDOHYDROLASE; BACTERIAL GENOMES; BIOINFORMATIC TOOLS; ENOLASE; ENZYMATIC ACTIVITIES; ENZYMATIC FUNCTIONS; ENZYME FUNCTIONS; ENZYME PRODUCTION; EXPERIMENTAL PROTOCOLS; GENOME PROJECTS; GLUTATHIONE TRANSFERASE; HALOALKANOIC ACID DEHALOGENASE; IN-VITRO; IN-VIVO; ISOPRENOIDS; PROTEIN PRODUCTION; RELIABLE FUNCTION; SCIENTIFIC COMMUNITY; STRUCTURE DETERMINATION; STRUCTURE-BASED; SYNTHASES; TARGET SELECTION;

EID: 81255138862     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201312u     Document Type: Review
Times cited : (148)

References (53)
  • 1
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies
    • Schnoes, A. M., Brown, S. D., Dodevski, I., and Babbitt, P. C. (2009) Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies PLoS Comput. Biol. 5, e1000605
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000605
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 2
    • 35848958144 scopus 로고    scopus 로고
    • A Protein Structure (or Function?) Initiative
    • Gerlt, J. A. (2007) A Protein Structure (or Function?) Initiative Structure 15, 1353-1356
    • (2007) Structure , vol.15 , pp. 1353-1356
    • Gerlt, J.A.1
  • 3
    • 0030667789 scopus 로고    scopus 로고
    • Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities
    • DOI 10.1074/jbc.272.49.30591
    • 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 (Pubitemid 27527485)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.49 , pp. 30591-30594
    • Babbitt, P.C.1    Gerlt, J.A.2
  • 4
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies
    • DOI 10.1146/annurev.biochem.70.1.209
    • 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 (Pubitemid 32662210)
    • (2001) Annual Review of Biochemistry , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 5
    • 9744279773 scopus 로고    scopus 로고
    • Divergent evolution in the enolase superfamily: The interplay of mechanism and specificity
    • DOI 10.1016/j.abb.2004.07.034, PII S0003986104004059
    • 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 (Pubitemid 39586583)
    • (2005) Archives of Biochemistry and Biophysics , vol.433 , Issue.1 , pp. 59-70
    • Gerlt, J.A.1    Babbitt, P.C.2    Rayment, I.3
  • 6
    • 81255198806 scopus 로고    scopus 로고
    • Divergent Evolution in the Enolase Superfamily: Strategies for Assigning Function
    • (in press)
    • Gerlt, J. A., Babbitt, P. C., Jacobson, M. P., and Almo, S. C. (2011) Divergent Evolution in the Enolase Superfamily: Strategies for Assigning Function J. Biol. Chem. 286, ZZZ (in press)
    • (2011) J. Biol. Chem. , vol.286
    • Gerlt, J.A.1    Babbitt, P.C.2    Jacobson, M.P.3    Almo, S.C.4
  • 7
    • 17844384785 scopus 로고    scopus 로고
    • Structural and catalytic diversity within the amidohydrolase superfamily
    • DOI 10.1021/bi047326v
    • Seibert, C. M. and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily Biochemistry 44, 6383-6391 (Pubitemid 40593789)
    • (2005) Biochemistry , vol.44 , Issue.17 , pp. 6383-6391
    • Seibert, C.M.1    Raushel, F.M.2
  • 8
    • 33745027619 scopus 로고    scopus 로고
    • A gold standard set of mechanistically diverse enzyme superfamilies
    • Brown, S. D., Gerlt, J. A., Seffernick, J. L., and Babbitt, P. C. (2006) A gold standard set of mechanistically diverse enzyme superfamilies Genome Biol. 7, R8
    • (2006) Genome Biol. , vol.7 , pp. 8
    • Brown, S.D.1    Gerlt, J.A.2    Seffernick, J.L.3    Babbitt, P.C.4
  • 9
    • 84864278347 scopus 로고    scopus 로고
    • Using sequence similarity networks for visualization of relationships across diverse protein superfamilies
    • Atkinson, H. J., Morris, J. H., Ferrin, T. E., and Babbitt, P. C. (2009) Using sequence similarity networks for visualization of relationships across diverse protein superfamilies PLoS One 4, e4345
    • (2009) PLoS One , vol.4 , pp. 4345
    • Atkinson, H.J.1    Morris, J.H.2    Ferrin, T.E.3    Babbitt, P.C.4
  • 10
    • 33644560639 scopus 로고    scopus 로고
    • Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database
    • Pegg, S. C., Brown, S. D., Ojha, S., Seffernick, J., Meng, E. C., Morris, J. H., Chang, P. J., Huang, C. C., Ferrin, T. E., and Babbitt, P. C. (2006) Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database Biochemistry 45, 2545-2355
    • (2006) Biochemistry , vol.45 , pp. 2545-2355
    • Pegg, S.C.1    Brown, S.D.2    Ojha, S.3    Seffernick, J.4    Meng, E.C.5    Morris, J.H.6    Chang, P.J.7    Huang, C.C.8    Ferrin, T.E.9    Babbitt, P.C.10
  • 12
    • 33749850046 scopus 로고    scopus 로고
    • Universal screening methods and applications of ThermoFluor
    • DOI 10.1177/1087057106292746
    • Cummings, M. D., Farnum, M. A., and Nelen, M. I. (2006) Universal screening methods and applications of ThermoFluor J. Biomol. Screening 11, 854-863 (Pubitemid 44562327)
    • (2006) Journal of Biomolecular Screening , vol.11 , Issue.7 , pp. 854-863
    • Cummings, M.D.1    Farnum, M.A.2    Nelen, M.I.3
  • 13
    • 33748929006 scopus 로고    scopus 로고
    • Thermofluor-based high-throughput stability optimization of proteins for structural studies
    • DOI 10.1016/j.ab.2006.07.027, PII S0003269706005355
    • Ericsson, U. B., Hallberg, B. M., Detitta, G. T., Dekker, N., and Nordlund, P. (2006) Thermofluor-based high throughput stability optimization of proteins for structural studies Anal. Biochem. 357, 289-298 (Pubitemid 44430091)
    • (2006) Analytical Biochemistry , vol.357 , Issue.2 , pp. 289-298
    • Ericsson, U.B.1    Hallberg, B.M.2    DeTitta, G.T.3    Dekker, N.4    Nordlund, P.5
  • 14
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • DOI 10.1126/science.1065659
    • Baker, D. and Sali, A. (2001) Protein structure prediction and structural genomics Science 294, 93-96 (Pubitemid 32952955)
    • (2001) Science , vol.294 , Issue.5540 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 15
    • 17744387920 scopus 로고    scopus 로고
    • All are not equal: A benchmark of different homology modeling programs
    • DOI 10.1110/ps.041253405
    • Wallner, B. and Elofsson, A. (2005) All are not equal: A benchmark of different homology modeling programs Protein Sci. 14, 1315-1327 (Pubitemid 40577811)
    • (2005) Protein Science , vol.14 , Issue.5 , pp. 1315-1327
    • Wallner, B.1    Elofsson, A.2
  • 20
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
    • DOI 10.1021/jm060999m
    • Leach, A. R., Shoichet, B. K., and Peishoff, C. E. (2006) Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps J. Med. Chem. 49, 5851-5855 (Pubitemid 44484931)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.20 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 21
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • DOI 10.1038/nature03197
    • Shoichet, B. K. (2004) Virtual screening of chemical libraries Nature 432, 862-865 (Pubitemid 40037142)
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 24
  • 25
    • 0031021397 scopus 로고    scopus 로고
    • Structure, catalytic mechanism, and evolution of the glutathione transferases
    • DOI 10.1021/tx960072x
    • Armstrong, R. N. (1997) Structure, catalytic mechanism, and evolution of the glutathione transferases Chem. Res. Toxicol. 10, 2-18 (Pubitemid 27044902)
    • (1997) Chemical Research in Toxicology , vol.10 , Issue.1 , pp. 2-18
    • Armstrong, R.N.1
  • 26
    • 0032175008 scopus 로고    scopus 로고
    • Mechanistic imperatives for the evolution of glutathione transferases
    • Armstrong, R. N. (1998) Mechanistic imperatives for the evolution of glutathione transferases Curr. Opin. Chem. Biol. 2, 618-623 (Pubitemid 128645719)
    • (1998) Current Opinion in Chemical Biology , vol.2 , Issue.5 , pp. 618-623
    • Armstrong, R.N.1
  • 27
    • 85012859170 scopus 로고    scopus 로고
    • Glutathione Transferases
    • In (Guengerich, F. P. Ed.) 2nd ed. pp, Elsevier Science, Oxford, U.K.
    • Armstrong, R. N. (2010) Glutathione Transferases. In Comprehensive Toxicology (Guengerich, F. P., Ed.) 2nd ed., pp 295-321, Elsevier Science, Oxford, U.K.
    • (2010) Comprehensive Toxicology , pp. 295-321
    • Armstrong, R.N.1
  • 28
    • 0345832239 scopus 로고    scopus 로고
    • Parallel Evolutionary Pathways for Glutathione Transferases: Structure and Mechanism of the Mitochondrial Class Kappa Enzyme rGSTK1-1
    • DOI 10.1021/bi035832z
    • Ladner, J. E., Parsons, J. F., Rife, C. L., Gilliland, G. L., and Armstrong, R. N. (2004) Parallel evolutionary pathways for glutathione transferases: Structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1 Biochemistry 43, 352-361 (Pubitemid 38082557)
    • (2004) Biochemistry , vol.43 , Issue.2 , pp. 352-361
    • Ladner, J.E.1    Parsons, J.F.2    Rife, C.L.3    Gilliland, G.L.4    Armstrong, R.N.5
  • 29
    • 34250211811 scopus 로고    scopus 로고
    • 2-Hydroxychromene-2-carboxylic acid isomerase: A kappa class glutathione transferase from Pseudomonas putida
    • DOI 10.1021/bi700356u
    • Thompson, L. C., Ladner, J. E., Codreanu, S. G., Harp, J., Gilliland, G. L., and Armstrong, R. N. (2007) 2-Hydroxychromene-2-carboxylic acid isomerase: A kappa class glutathione transferase from Pseudomonas putida Biochemistry 46, 6710-6722 (Pubitemid 46906402)
    • (2007) Biochemistry , vol.46 , Issue.23 , pp. 6710-6722
    • Thompson, L.C.1    Ladner, J.E.2    Codreanu, S.G.3    Harp, J.4    Gilliland, G.L.5    Armstrong, R.N.6
  • 30
    • 72749084211 scopus 로고    scopus 로고
    • An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations
    • Atkinson, H. J. and Babbitt, P. C. (2009) An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations PLoS Comput. Biol. 5, e1000541
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000541
    • Atkinson, H.J.1    Babbitt, P.C.2
  • 31
    • 72749095187 scopus 로고    scopus 로고
    • Glutathione transferases are structural and functional outliers in the thioredoxin fold
    • Atkinson, H. J. and Babbitt, P. C. (2009) Glutathione transferases are structural and functional outliers in the thioredoxin fold Biochemistry 48, 11108-11116
    • (2009) Biochemistry , vol.48 , pp. 11108-11116
    • Atkinson, H.J.1    Babbitt, P.C.2
  • 32
    • 67650492703 scopus 로고    scopus 로고
    • Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase
    • Wadington, M. C., Ladner, J. E., Stourman, N. V., Harp, J. M., and Armstrong, R. N. (2009) Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase Biochemistry 48, 6559-6561
    • (2009) Biochemistry , vol.48 , pp. 6559-6561
    • Wadington, M.C.1    Ladner, J.E.2    Stourman, N.V.3    Harp, J.M.4    Armstrong, R.N.5
  • 33
    • 79951590036 scopus 로고    scopus 로고
    • Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli
    • Stourman, N. V., Branch, M. C., Schaab, M. R., Harp, J. M., Ladner, J. E., and Armstrong, R. N. (2011) Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli Biochemistry 50, 1274-1281
    • (2011) Biochemistry , vol.50 , pp. 1274-1281
    • Stourman, N.V.1    Branch, M.C.2    Schaab, M.R.3    Harp, J.M.4    Ladner, J.E.5    Armstrong, R.N.6
  • 34
    • 1542267779 scopus 로고    scopus 로고
    • Analysis of the Substrate Specificity Loop of the HAD Superfamily Cap Domain
    • DOI 10.1021/bi0356810
    • Lahiri, S. D., Zhang, G., Dai, J., Dunaway-Mariano, D., and Allen, K. N. (2004) Analysis of the substrate specificity loop of the HAD superfamily cap domain Biochemistry 43, 2812-2820 (Pubitemid 38327812)
    • (2004) Biochemistry , vol.43 , Issue.10 , pp. 2812-2820
    • Lahiri, S.D.1    Zhang, G.2    Dai, J.3    Dunaway-Mariano, D.4    Allen, K.N.5
  • 35
    • 4344585269 scopus 로고    scopus 로고
    • Phosphoryl group transfer: Evolution of a catalytic scaffold
    • DOI 10.1016/j.tibs.2004.07.008, PII S0968000404001793
    • Allen, K. N. and Dunaway-Mariano, D. (2004) Phosphoryl group transfer: Evolution of a catalytic scaffold Trends Biochem. Sci. 29, 495-503 (Pubitemid 39158873)
    • (2004) Trends in Biochemical Sciences , vol.29 , Issue.9 , pp. 495-503
    • Allen, K.N.1    Dunaway-Mariano, D.2
  • 36
    • 33746922036 scopus 로고    scopus 로고
    • Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes
    • DOI 10.1016/j.jmb.2006.06.049, PII S0022283606007777
    • Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D., and Aravind, L. (2006) Evolutionary genomics of the HAD superfamily: Understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes J. Mol. Biol. 361, 1003-1034 (Pubitemid 44192587)
    • (2006) Journal of Molecular Biology , vol.361 , Issue.5 , pp. 1003-1034
    • Burroughs, A.M.1    Allen, K.N.2    Dunaway-Mariano, D.3    Aravind, L.4
  • 37
    • 44449119913 scopus 로고    scopus 로고
    • The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state
    • DOI 10.1073/pnas.0710800105
    • Lu, Z., Dunaway-Mariano, D., and Allen, K. N. (2008) The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state Proc. Natl. Acad. Sci. U.S.A. 105, 5687-5692 (Pubitemid 351758433)
    • (2008) Proceedings of the National Academy of Sciences of the United States of America , vol.105 , Issue.15 , pp. 5687-5692
    • Lu, Z.1    Dunaway-Mariano, D.2    Allen, K.N.3
  • 38
    • 33845400832 scopus 로고    scopus 로고
    • Farnesyl diphosphate synthase: The art of compromise between substrate selectivity and stereoselectivity
    • DOI 10.1021/ja065573b
    • Thulasiram, H. V. and Poulter, C. D. (2006) Farnesyl diphosphate synthase: The art of compromise between substrate selectivity and stereoselectivity J. Am. Chem. Soc. 128, 15819-15823 (Pubitemid 44894122)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.49 , pp. 15819-15823
    • Thulasiram, H.V.1    Poulter, C.D.2
  • 39
    • 34147178365 scopus 로고    scopus 로고
    • Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis
    • DOI 10.1126/science.1137786
    • Thulasiram, H. V., Erickson, H. K., and Poulter, C. D. (2007) Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis Science 316, 73-76 (Pubitemid 46559519)
    • (2007) Science , vol.316 , Issue.5821 , pp. 73-76
    • Thulasiram, H.V.1    Erickson, H.K.2    Poulter, C.D.3
  • 43
    • 34547939672 scopus 로고    scopus 로고
    • Structure-based activity prediction for an enzyme of unknown function
    • DOI 10.1038/nature05981, PII NATURE05981
    • Hermann, J. C., Marti-Arbona, R., Fedorov, A. A., Fedorov, E., Almo, S. C., Shoichet, B. K., and Raushel, F. M. (2007) Structure-based activity prediction for an enzyme of unknown function Nature 448, 775-779 (Pubitemid 47266333)
    • (2007) Nature , vol.448 , Issue.7155 , pp. 775-779
    • Hermann, J.C.1    Marti-Arbona, R.2    Fedorov, A.A.3    Fedorov, E.4    Almo, S.C.5    Shoichet, B.K.6    Raushel, F.M.7
  • 44
    • 79958097953 scopus 로고    scopus 로고
    • The moderately efficient enzyme: Evolutionary and physicochemical trends shaping enzyme parameters
    • Bar-Even, A., Noor, E., Savir, Y., Liebermeister, W., Davidi, D., Tawfik, D. S., and Milo, R. (2011) The moderately efficient enzyme: Evolutionary and physicochemical trends shaping enzyme parameters Biochemistry 50, 4402-4410
    • (2011) Biochemistry , vol.50 , pp. 4402-4410
    • Bar-Even, A.1    Noor, E.2    Savir, Y.3    Liebermeister, W.4    Davidi, D.5    Tawfik, D.S.6    Milo, R.7
  • 45
    • 64349121094 scopus 로고    scopus 로고
    • Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily
    • Xiang, D. F., Kolb, P., Fedorov, A. A., Meier, M. M., Fedorov, L. V., Nguyen, T. T., Sterner, R., Almo, S. C., Shoichet, B. K., and Raushel, F. M. (2009) Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily Biochemistry 48, 2237-2247
    • (2009) Biochemistry , vol.48 , pp. 2237-2247
    • Xiang, D.F.1    Kolb, P.2    Fedorov, A.A.3    Meier, M.M.4    Fedorov, L.V.5    Nguyen, T.T.6    Sterner, R.7    Almo, S.C.8    Shoichet, B.K.9    Raushel, F.M.10
  • 51
    • 77952411134 scopus 로고    scopus 로고
    • Studying enzyme-substrate specificity in silico: A case study of the Escherichia coli glycolysis pathway
    • Kalyanaraman, C. and Jacobson, M. P. (2010) Studying enzyme-substrate specificity in silico: A case study of the Escherichia coli glycolysis pathway Biochemistry 49, 4003-4005
    • (2010) Biochemistry , vol.49 , pp. 4003-4005
    • Kalyanaraman, C.1    Jacobson, M.P.2
  • 52
    • 33645677238 scopus 로고    scopus 로고
    • Evolution of enzymatic activities in the enolase superfamily: N-Succinylamino acid racemase and a new pathway for the irreversible conversion of d - To l -amino acids
    • Sakai, A., Xiang, D. F., Xu, C., Song, L., Yew, W. S., Raushel, F. M., and Gerlt, J. A. (2006) Evolution of enzymatic activities in the enolase superfamily: N-Succinylamino acid racemase and a new pathway for the irreversible conversion of d-to l -amino acids Biochemistry 45, 4455-4462
    • (2006) Biochemistry , vol.45 , pp. 4455-4462
    • Sakai, A.1    Xiang, D.F.2    Xu, C.3    Song, L.4    Yew, W.S.5    Raushel, F.M.6    Gerlt, J.A.7
  • 53
    • 54849415447 scopus 로고    scopus 로고
    • Mechanistic diversity in the RuBisCO superfamily: A novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum
    • Imker, H. J., Singh, J., Warlick, B. P., Tabita, F. R., and Gerlt, J. A. (2008) Mechanistic diversity in the RuBisCO superfamily: A novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum Biochemistry 47, 11171-11173
    • (2008) Biochemistry , vol.47 , pp. 11171-11173
    • Imker, H.J.1    Singh, J.2    Warlick, B.P.3    Tabita, F.R.4    Gerlt, J.A.5


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