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Volumn 425, Issue 8, 2013, Pages 1378-1389

Janus: Prediction and ranking of mutations required for functional interconversion of enzymes

Author keywords

bioinformatics; computational modeling; directed evolution; enzymology; protein engineering

Indexed keywords

ASPARTATE AMINOTRANSFERASE; TYROSINE AMINOTRANSFERASE;

EID: 84875734662     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.01.034     Document Type: Article
Times cited : (23)

References (38)
  • 1
    • 83755195482 scopus 로고    scopus 로고
    • Catalytic contributions from remote regions of enzyme structure
    • J. Lee, and N.M. Goodey Catalytic contributions from remote regions of enzyme structure Chem. Rev. 111 2011 7595 7624
    • (2011) Chem. Rev. , vol.111 , pp. 7595-7624
    • Lee, J.1    Goodey, N.M.2
  • 2
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 3
    • 3242891674 scopus 로고    scopus 로고
    • SDPpred: A tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins
    • O.V. Kalinina, P.S. Novichkov, A.A. Mironov, M.S. Gelfand, and A.B. Rakhmaninova SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins Nucleic Acids Res. 32 2004 W424 W428
    • (2004) Nucleic Acids Res. , vol.32
    • Kalinina, O.V.1    Novichkov, P.S.2    Mironov, A.A.3    Gelfand, M.S.4    Rakhmaninova, A.B.5
  • 4
    • 46249099576 scopus 로고    scopus 로고
    • Characterization and prediction of residues determining protein functional specificity
    • J.A. Capra, and M. Singh Characterization and prediction of residues determining protein functional specificity Bioinformatics 24 2008 1473 1480
    • (2008) Bioinformatics , vol.24 , pp. 1473-1480
    • Capra, J.A.1    Singh, M.2
  • 5
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • S.W. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 1999 295 299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 6
    • 23144436395 scopus 로고    scopus 로고
    • WebProAnalyst: An interactive tool for analysis of quantitative structure-activity relationships in protein families
    • V.A. Ivanisenko, A.M. Eroshkin, and N.A. Kolchanov WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families Nucleic Acids Res. 33 2005 W99 W104
    • (2005) Nucleic Acids Res. , vol.33
    • Ivanisenko, V.A.1    Eroshkin, A.M.2    Kolchanov, N.A.3
  • 8
    • 3242881590 scopus 로고    scopus 로고
    • CRASP: A program for analysis of coordinated substitutions in multiple alignments of protein sequences
    • D.A. Afonnikov, and N.A. Kolchanov CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences Nucleic Acids Res. 32 2004 W64 W68
    • (2004) Nucleic Acids Res. , vol.32
    • Afonnikov, D.A.1    Kolchanov, N.A.2
  • 9
    • 0029079958 scopus 로고
    • Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis
    • J.J. Onuffer, and J.F. Kirsch Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis Protein Sci. 4 1995 1750 1757
    • (1995) Protein Sci. , vol.4 , pp. 1750-1757
    • Onuffer, J.J.1    Kirsch, J.F.2
  • 10
    • 0037470619 scopus 로고    scopus 로고
    • How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase
    • S.C. Rothman, and J.F. Kirsch How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase J. Mol. Biol. 327 2003 593 608
    • (2003) J. Mol. Biol. , vol.327 , pp. 593-608
    • Rothman, S.C.1    Kirsch, J.F.2
  • 11
    • 4944240750 scopus 로고    scopus 로고
    • Narrowing substrate specificity in a directly evolved enzyme: The A293D mutant of aspartate aminotransferase
    • M.A. Chow, K.E. McElroy, K.D. Corbett, J.M. Berger, and J.F. Kirsch Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase Biochemistry 43 2004 12780 12787
    • (2004) Biochemistry , vol.43 , pp. 12780-12787
    • Chow, M.A.1    McElroy, K.E.2    Corbett, K.D.3    Berger, J.M.4    Kirsch, J.F.5
  • 12
    • 1342310509 scopus 로고    scopus 로고
    • Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase
    • S.C. Rothman, M. Voorhies, and J.F. Kirsch Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase Protein Sci. 13 2004 763 772
    • (2004) Protein Sci. , vol.13 , pp. 763-772
    • Rothman, S.C.1    Voorhies, M.2    Kirsch, J.F.3
  • 13
    • 0028908425 scopus 로고
    • Decreasing the basicity of the active-site base, LYS-258, of Escherichia coli aspartate aminotransferase by replacement with γ-thialysine
    • L.M. Gloss, and J.F. Kirsch Decreasing the basicity of the active-site base, LYS-258, of Escherichia coli aspartate aminotransferase by replacement with γ-thialysine Biochemistry 34 1995 3990 3998
    • (1995) Biochemistry , vol.34 , pp. 3990-3998
    • Gloss, L.M.1    Kirsch, J.F.2
  • 14
    • 0035106702 scopus 로고    scopus 로고
    • A general method for the quantitative analysis of functional chimeras: Applications from site-directed mutagenesis and macromolecular association
    • T.N. Luong, and J.F. Kirsch A general method for the quantitative analysis of functional chimeras: applications from site-directed mutagenesis and macromolecular association Protein Sci. 10 2001 581 591
    • (2001) Protein Sci. , vol.10 , pp. 581-591
    • Luong, T.N.1    Kirsch, J.F.2
  • 15
    • 0025366034 scopus 로고
    • Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity
    • S. Kuramitsu, K. Hiromi, H. Hayashi, Y. Morino, and H. Kagamiyama Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity Biochemistry 29 1990 5469 5476
    • (1990) Biochemistry , vol.29 , pp. 5469-5476
    • Kuramitsu, S.1    Hiromi, K.2    Hayashi, H.3    Morino, Y.4    Kagamiyama, H.5
  • 16
    • 0027420413 scopus 로고
    • Escherichia coli aromatic amino acid aminotransferase: Characterization and comparison with aspartate aminotransferase
    • H. Hayashi, K. Inoue, T. Nagata, S. Kuramitsu, and H. Kagamiyama Escherichia coli aromatic amino acid aminotransferase: characterization and comparison with aspartate aminotransferase Biochemistry 32 1993 12229 12239
    • (1993) Biochemistry , vol.32 , pp. 12229-12239
    • Hayashi, H.1    Inoue, K.2    Nagata, T.3    Kuramitsu, S.4    Kagamiyama, H.5
  • 17
    • 0036892433 scopus 로고    scopus 로고
    • Quantitative chimeric analysis of six specificity determinants that differentiate Escherichia coli aspartate from tyrosine aminotransferase
    • W.A. Shaffer, T.N. Luong, S.C. Rothman, and J.F. Kirsch Quantitative chimeric analysis of six specificity determinants that differentiate Escherichia coli aspartate from tyrosine aminotransferase Protein Sci. 11 2002 2848 2859
    • (2002) Protein Sci. , vol.11 , pp. 2848-2859
    • Shaffer, W.A.1    Luong, T.N.2    Rothman, S.C.3    Kirsch, J.F.4
  • 18
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 20
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • W.P.C. Stemmer Rapid evolution of a protein in vitro by DNA shuffling Nature 370 1994 389 391
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.C.1
  • 21
    • 0022550466 scopus 로고
    • The cloning and sequence analysis of the aspc and tyrb genes from Escherichia coli-K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes
    • I.G. Fotheringham, S.A. Dacey, P.P. Taylor, T.J. Smith, M.G. Hunter, and M.E. Finlay The cloning and sequence analysis of the aspc and tyrb genes from Escherichia coli-K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes Biochem. J. 234 1986 593 604
    • (1986) Biochem. J. , vol.234 , pp. 593-604
    • Fotheringham, I.G.1    Dacey, S.A.2    Taylor, P.P.3    Smith, T.J.4    Hunter, M.G.5    Finlay, M.E.6
  • 23
    • 78650905964 scopus 로고    scopus 로고
    • Rosetta3: An object-oriented software suite for the simulation and design of macromolecules
    • M.L. Johnson, L. Brand, Elsevier Academic Press. Inc. San Diego, CA
    • A. Leaver-Fay, M. Tyka, S.M. Lewis, O.F. Lange, J. Thompson, and R. Jacak Rosetta3: an object-oriented software suite for the simulation and design of macromolecules M.L. Johnson, L. Brand, Methods in Enzymology, Volume 487: Computer Methods, Part C 2011 Elsevier Academic Press. Inc. San Diego, CA 545 574
    • (2011) Methods in Enzymology, Volume 487: Computer Methods, Part C , pp. 545-574
    • Leaver-Fay, A.1    Tyka, M.2    Lewis, S.M.3    Lange, O.F.4    Thompson, J.5    Jacak, R.6
  • 24
    • 0028174289 scopus 로고
    • Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms
    • J. Jager, M. Moser, U. Sauder, and J.N. Jansonius Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms. J. Mol. Biol. 239 1994 285 305
    • (1994) J. Mol. Biol. , vol.239 , pp. 285-305
    • Jager, J.1    Moser, M.2    Sauder, U.3    Jansonius, J.N.4
  • 25
    • 0029124159 scopus 로고
    • Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase
    • V.N. Malashkevich, J.J. Onuffer, J.F. Kirsch, and J.N. Jansonius Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase Nat. Struct. Biol. 2 1995 548 553
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 548-553
    • Malashkevich, V.N.1    Onuffer, J.J.2    Kirsch, J.F.3    Jansonius, J.N.4
  • 26
    • 0032540849 scopus 로고    scopus 로고
    • Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: A substrate recognition site constructed by rearrangement of hydrogen bond network
    • A. Okamoto, Y. Nakai, H. Hayashi, K. Hirotsu, and H. Kagamiyama Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network J. Mol. Biol. 280 1998 443 461
    • (1998) J. Mol. Biol. , vol.280 , pp. 443-461
    • Okamoto, A.1    Nakai, Y.2    Hayashi, H.3    Hirotsu, K.4    Kagamiyama, H.5
  • 27
    • 77957316716 scopus 로고    scopus 로고
    • An exciting but challenging road ahead for computational enzyme design
    • D. Baker An exciting but challenging road ahead for computational enzyme design Protein Sci. 19 2010 1817 1819
    • (2010) Protein Sci. , vol.19 , pp. 1817-1819
    • Baker, D.1
  • 30
    • 0141908152 scopus 로고    scopus 로고
    • Chimeric gene library construction by a simple and highly versatile method using recombination-dependent exponential amplification
    • A. Ikeuchi, Y. Kawarasaki, T. Shinbata, and T. Yamane Chimeric gene library construction by a simple and highly versatile method using recombination-dependent exponential amplification Biotechnol. Prog. 19 2003 1460 1467
    • (2003) Biotechnol. Prog. , vol.19 , pp. 1460-1467
    • Ikeuchi, A.1    Kawarasaki, Y.2    Shinbata, T.3    Yamane, T.4
  • 32
    • 0021932743 scopus 로고
    • D-2-Hydroxyisocaproate dehydrogenase from Lactobacillus casei: A new enzyme suitable for stereospecific reduction of 2-ketocarboxylic acids
    • W. Hummel, H. Schutte, and M.R. Kula d-2-Hydroxyisocaproate dehydrogenase from Lactobacillus casei: a new enzyme suitable for stereospecific reduction of 2-ketocarboxylic acids Appl. Microbiol. Biotechnol. 21 1985 7 15
    • (1985) Appl. Microbiol. Biotechnol. , vol.21 , pp. 7-15
    • Hummel, W.1    Schutte, H.2    Kula, M.R.3
  • 35
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • J. Soding Protein homology detection by HMM-HMM comparison Bioinformatics 21 2005 951 960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 36
    • 77149179401 scopus 로고    scopus 로고
    • NMR structure determination for larger proteins using backbone-only data
    • S. Raman, O.F. Lange, P. Rossi, M. Tyka, X. Wang, and J. Aramini NMR structure determination for larger proteins using backbone-only data Science 327 2010 1014 1018
    • (2010) Science , vol.327 , pp. 1014-1018
    • Raman, S.1    Lange, O.F.2    Rossi, P.3    Tyka, M.4    Wang, X.5    Aramini, J.6
  • 37
    • 79960078022 scopus 로고    scopus 로고
    • Incorporation of evolutionary information into Rosetta comparative modeling
    • J. Thompson, and D. Baker Incorporation of evolutionary information into Rosetta comparative modeling Proteins: Struct., Funct., Bioinf. 79 2011 2380 2388
    • (2011) Proteins: Struct., Funct., Bioinf. , vol.79 , pp. 2380-2388
    • Thompson, J.1    Baker, D.2


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