메뉴 건너뛰기




Volumn 52, Issue 42, 2013, Pages 7428-7438

A substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; AMINO ACIDS; CARBON; CATALYSIS; COVALENT BONDS; HYDROLYSIS; NUCLEOPHILES; PROTON TRANSFER; QUANTUM CHEMISTRY;

EID: 84886788495     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401156a     Document Type: Article
Times cited : (9)

References (33)
  • 1
    • 0017807931 scopus 로고
    • Purification and properties of 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase from two strains of Pseudomonas putida
    • Bayly, R. C. and di Berardino, D. (1978) Purification and properties of 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase from two strains of Pseudomonas putida J. Bacteriol. 134, 30-37
    • (1978) J. Bacteriol. , vol.134 , pp. 30-37
    • Bayly, R.C.1    Di Berardino, D.2
  • 2
    • 84858244926 scopus 로고    scopus 로고
    • Identification of an acyl-enzyme intermediate in a meta-cleavage product hydrolase reveals the versatility of the catalytic triad
    • Ruzzini, A. C., Ghosh, S., Horsman, G. P., Foster, L. J., Bolin, J. T., and Eltis, L. D. (2012) Identification of an acyl-enzyme intermediate in a meta-cleavage product hydrolase reveals the versatility of the catalytic triad J. Am. Chem. Soc. 134, 4615-4624
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 4615-4624
    • Ruzzini, A.C.1    Ghosh, S.2    Horsman, G.P.3    Foster, L.J.4    Bolin, J.T.5    Eltis, L.D.6
  • 3
    • 84864268097 scopus 로고    scopus 로고
    • The catalytic serine of meta-cleavage product hydrolases is activated differently for C-O bond cleavage than for C-C bond cleavage
    • Ruzzini, A. C., Horsman, G. P., and Eltis, L. D. (2012) The catalytic serine of meta-cleavage product hydrolases is activated differently for C-O bond cleavage than for C-C bond cleavage Biochemistry 51, 5831-5840
    • (2012) Biochemistry , vol.51 , pp. 5831-5840
    • Ruzzini, A.C.1    Horsman, G.P.2    Eltis, L.D.3
  • 4
    • 0034285515 scopus 로고    scopus 로고
    • Alpha/Beta-hydrolase fold enzymes: Structures, functions and mechanisms
    • Holmquist, M. (2000) Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms Curr. Protein Pept. Sci. 1, 209-235
    • (2000) Curr. Protein Pept. Sci. , vol.1 , pp. 209-235
    • Holmquist, M.1
  • 5
    • 10044248344 scopus 로고    scopus 로고
    • Catalytic promiscuity in biocatalysis: Using old enzymes to form new bonds and follow new pathways
    • Bornscheuer, U. T. and Kazlauskas, R. J. (2004) Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways Angew. Chem., Int. Ed. Engl. 43, 6032-6040
    • (2004) Angew. Chem., Int. Ed. Engl. , vol.43 , pp. 6032-6040
    • Bornscheuer, U.T.1    Kazlauskas, R.J.2
  • 6
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom, L. (2002) Serine protease mechanism and specificity Chem. Rev. 102, 4501-4524
    • (2002) Chem. Rev. , vol.102 , pp. 4501-4524
    • Hedstrom, L.1
  • 7
    • 21744450137 scopus 로고    scopus 로고
    • Emergent mechanistic diversity of enzyme-catalysed beta-diketone cleavage
    • Grogan, G. (2005) Emergent mechanistic diversity of enzyme-catalysed beta-diketone cleavage Biochem. J. 388, 721-730
    • (2005) Biochem. J. , vol.388 , pp. 721-730
    • Grogan, G.1
  • 8
    • 80054710066 scopus 로고    scopus 로고
    • Structure, mechanism, and substrate specificity of kynureninase
    • Phillips, R. S. (2011) Structure, mechanism, and substrate specificity of kynureninase Biochim. Biophys. Acta 1814, 1481-1488
    • (2011) Biochim. Biophys. Acta , vol.1814 , pp. 1481-1488
    • Phillips, R.S.1
  • 9
    • 0030776495 scopus 로고    scopus 로고
    • Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase
    • Lam, W. W. and Bugg, T. D. (1997) Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9- dioic acid 5,6-hydrolase Biochemistry 36, 12242-12251
    • (1997) Biochemistry , vol.36 , pp. 12242-12251
    • Lam, W.W.1    Bugg, T.D.2
  • 10
    • 4644237751 scopus 로고    scopus 로고
    • Enzymatic reactions involving novel mechanisms of carbanion stabilization
    • Begley, T. P. and Ealick, S. E. (2004) Enzymatic reactions involving novel mechanisms of carbanion stabilization Curr. Opin. Chem. Biol. 8, 508-515
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 508-515
    • Begley, T.P.1    Ealick, S.E.2
  • 11
    • 38849119713 scopus 로고    scopus 로고
    • Carbon isotope effect study on orotidine 5′-monophosphate decarboxylase: Support for an anionic intermediate
    • Van Vleet, J. L., Reinhardt, L. A., Miller, B. G., Sievers, A., and Cleland, W. W. (2008) Carbon isotope effect study on orotidine 5′-monophosphate decarboxylase: support for an anionic intermediate Biochemistry 47, 798-803
    • (2008) Biochemistry , vol.47 , pp. 798-803
    • Van Vleet, J.L.1    Reinhardt, L.A.2    Miller, B.G.3    Sievers, A.4    Cleland, W.W.5
  • 12
    • 33748762789 scopus 로고    scopus 로고
    • Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway
    • Horsman, G. P., Ke, J., Dai, S., Seah, S. Y., Bolin, J. T., and Eltis, L. D. (2006) Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway Biochemistry 45, 11071-11086
    • (2006) Biochemistry , vol.45 , pp. 11071-11086
    • Horsman, G.P.1    Ke, J.2    Dai, S.3    Seah, S.Y.4    Bolin, J.T.5    Eltis, L.D.6
  • 13
    • 12744274585 scopus 로고    scopus 로고
    • Stereochemistry of the reaction catalysed by 2-hydroxy-6-keto-6-phenyl- hexa-2,4-dienoic acid 5,6-hydrolase (BphD)
    • Li, J. J. and Bugg, T. D. (2005) Stereochemistry of the reaction catalysed by 2-hydroxy-6-keto-6-phenyl-hexa-2,4-dienoic acid 5,6-hydrolase (BphD) Chem. Commun. (Cambridge, U. K.) 130-132
    • (2005) Chem. Commun. (Cambridge, U. K.) , pp. 130-132
    • Li, J.J.1    Bugg, T.D.2
  • 14
    • 34547094599 scopus 로고    scopus 로고
    • The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad
    • Horsman, G. P., Bhowmik, S., Seah, S. Y., Kumar, P., Bolin, J. T., and Eltis, L. D. (2007) The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad J. Biol. Chem. 282, 19894-19904
    • (2007) J. Biol. Chem. , vol.282 , pp. 19894-19904
    • Horsman, G.P.1    Bhowmik, S.2    Seah, S.Y.3    Kumar, P.4    Bolin, J.T.5    Eltis, L.D.6
  • 15
    • 73649123859 scopus 로고    scopus 로고
    • Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism
    • Lack, N. A., Yam, K. C., Lowe, E. D., Horsman, G. P., Owen, R. L., Sim, E., and Eltis, L. D. (2010) Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism J. Biol. Chem. 285, 434-443
    • (2010) J. Biol. Chem. , vol.285 , pp. 434-443
    • Lack, N.A.1    Yam, K.C.2    Lowe, E.D.3    Horsman, G.P.4    Owen, R.L.5    Sim, E.6    Eltis, L.D.7
  • 16
    • 0040684811 scopus 로고    scopus 로고
    • Chemical and biochemical properties of 2-hydroxypentadienoic acid, a homologue of enolpyruvic acid
    • Pollard, J. R., Henderson, I. M. J., and Bugg, T. D. H. (1997) Chemical and biochemical properties of 2-hydroxypentadienoic acid, a homologue of enolpyruvic acid Chem. Commun. 1885-1886
    • (1997) Chem. Commun. , pp. 1885-1886
    • Pollard, J.R.1    Henderson, I.M.J.2    Bugg, T.D.H.3
  • 17
    • 84882661067 scopus 로고    scopus 로고
    • The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites
    • Ruzzini, A. C., Bhowmik, S., Yam, K. C., Ghosh, S., Bolin, J. T., and Eltis, L. D. (2013) The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites Biochemistry 52, 5685-5695
    • (2013) Biochemistry , vol.52 , pp. 5685-5695
    • Ruzzini, A.C.1    Bhowmik, S.2    Yam, K.C.3    Ghosh, S.4    Bolin, J.T.5    Eltis, L.D.6
  • 18
    • 0034717267 scopus 로고    scopus 로고
    • Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls
    • Seah, S. Y., Labbe, G., Nerdinger, S., Johnson, M. R., Snieckus, V., and Eltis, L. D. (2000) Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls J. Biol. Chem. 275, 15701-15708
    • (2000) J. Biol. Chem. , vol.275 , pp. 15701-15708
    • Seah, S.Y.1    Labbe, G.2    Nerdinger, S.3    Johnson, M.R.4    Snieckus, V.5    Eltis, L.D.6
  • 20
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray Diffraction Data Collected in Oscillation Mode
    • Academic Press, New York
    • Otwinowski, Z. and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode, in Methods in Enzymology, pp 307-326, Academic Press, New York.
    • (1997) Methods in Enzymology , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 24
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr., Sect. A: Found. Crystallogr. 47 (Pt 2) 110-119
    • (1991) Acta Crystallogr., Sect. A: Found. Crystallogr. , vol.47 , Issue.PART 2 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 26
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26, 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.3    Thornton, J.M.4
  • 27
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J. M., Lovell, S. C., Richardson, J. S., and Richardson, D. C. (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285, 1735-1747
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 28
    • 34249790861 scopus 로고    scopus 로고
    • Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites
    • Seah, S. Y., Ke, J., Denis, G., Horsman, G. P., Fortin, P. D., Whiting, C. J., and Eltis, L. D. (2007) Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites J. Bacteriol. 189, 4038-4045
    • (2007) J. Bacteriol. , vol.189 , pp. 4038-4045
    • Seah, S.Y.1    Ke, J.2    Denis, G.3    Horsman, G.P.4    Fortin, P.D.5    Whiting, C.J.6    Eltis, L.D.7
  • 29
    • 84882661067 scopus 로고    scopus 로고
    • The lid domain of the MCP hydrolase DxnB2 contributes to an increased specificity for recalcitrant PCB metabolites
    • Ruzzini, A. C., Bhowmik, S., Ghosh, S., Bolin, J. T., and Eltis, L. D. (2013) The lid domain of the MCP hydrolase DxnB2 contributes to an increased specificity for recalcitrant PCB metabolites Biochemistry 52 (33) 5685-5695
    • (2013) Biochemistry , vol.52 , Issue.33 , pp. 5685-5695
    • Ruzzini, A.C.1    Bhowmik, S.2    Ghosh, S.3    Bolin, J.T.4    Eltis, L.D.5
  • 30
    • 2542616771 scopus 로고    scopus 로고
    • Sequence and structure of epoxide hydrolases: A systematic analysis
    • Barth, S., Fischer, M., Schmid, R. D., and Pleiss, J. (2004) Sequence and structure of epoxide hydrolases: a systematic analysis Proteins 55, 846-855
    • (2004) Proteins , vol.55 , pp. 846-855
    • Barth, S.1    Fischer, M.2    Schmid, R.D.3    Pleiss, J.4
  • 31
    • 0036403514 scopus 로고    scopus 로고
    • 2-hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: Evidence from 18O isotope exchange for gem-diol intermediate
    • Bugg, T. D., Fleming, S. M., Robertson, T. A., and Langley, G. J. (2002) 2-hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: evidence from 18O isotope exchange for gem-diol intermediate Methods Enzymol. 354, 106-118
    • (2002) Methods Enzymol. , vol.354 , pp. 106-118
    • Bugg, T.D.1    Fleming, S.M.2    Robertson, T.A.3    Langley, G.J.4
  • 32
    • 0026925802 scopus 로고
    • NMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins
    • Liepinsh, E., Otting, G., and Wuthrich, K. (1992) NMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins J. Biomol. NMR 2, 447-465
    • (1992) J. Biomol. NMR , vol.2 , pp. 447-465
    • Liepinsh, E.1    Otting, G.2    Wuthrich, K.3
  • 33
    • 0017290637 scopus 로고
    • Mechanism and specificity of succinyl-CoA:3-ketoacid coenzyme A transferase
    • White, H. and Jencks, W. P. (1976) Mechanism and specificity of succinyl-CoA:3-ketoacid coenzyme A transferase J. Biol. Chem. 251, 1688-1699
    • (1976) J. Biol. Chem. , vol.251 , pp. 1688-1699
    • White, H.1    Jencks, W.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.