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Volumn 44, Issue 23, 2005, Pages 8207-8217

Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: A role for Ser-110 in deacylation

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CATALYSIS; CRYSTAL STRUCTURE; ENZYME INHIBITION; ENZYMES; HYDROGEN BONDS; HYDROLYSIS; POLYPEPTIDES;

EID: 20444369942     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0473004     Document Type: Article
Times cited : (75)

References (47)
  • 1
    • 0020972419 scopus 로고
    • Penicillin-binding proteins and the mechanism of action of β-lactam antibiotics
    • Waxman, D. J., and Strominger, J. L. (1983) Penicillin-binding proteins and the mechanism of action of β-lactam antibiotics, Annu. Rev. Biochem. 52, 825-869.
    • (1983) Annu. Rev. Biochem. , vol.52 , pp. 825-869
    • Waxman, D.J.1    Strominger, J.L.2
  • 2
    • 0026049801 scopus 로고
    • Serine β-lactamases and penicillin-binding proteins
    • Ghuysen, J. M. (1991) Serine β-lactamases and penicillin-binding proteins, Annu. Rev. Microbiol. 45, 37-67.
    • (1991) Annu. Rev. Microbiol. , vol.45 , pp. 37-67
    • Ghuysen, J.M.1
  • 3
    • 0031736387 scopus 로고    scopus 로고
    • Multimodular penicillin-binding proteins: An enigmatic family of orthologs and paralogs
    • Goffin, C., and Ghuysen, J. M. (1998) Multimodular penicillin-binding proteins: An enigmatic family of orthologs and paralogs, Microbiol. Mol. Biol. Rev. 62, 1079-1093.
    • (1998) Microbiol. Mol. Biol. Rev. , vol.62 , pp. 1079-1093
    • Goffin, C.1    Ghuysen, J.M.2
  • 4
    • 0028173341 scopus 로고
    • Molecular structures of penicillin-binding proteins and β-lactamases
    • Ghuysen, J. M. (1994) Molecular structures of penicillin-binding proteins and β-lactamases, Trends Microbiol. 2, 372-380.
    • (1994) Trends Microbiol. , vol.2 , pp. 372-380
    • Ghuysen, J.M.1
  • 5
    • 0037858060 scopus 로고    scopus 로고
    • Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli
    • Holtje, J. V. (1998) Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli, Microbiol. Mol. Biol. Rev. 62, 181-203.
    • (1998) Microbiol. Mol. Biol. Rev. , vol.62 , pp. 181-203
    • Holtje, J.V.1
  • 6
    • 0013808622 scopus 로고
    • Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-D-alanine
    • Tipper, D. J., and Strominger, J. L. (1965) Mechanism of action of penicillins: A proposal based on their structural similarity to acyl-D-alanyl-D-alanine, Proc. Natl. Acad. Sci. U.S.A. 54, 1133-1141.
    • (1965) Proc. Natl. Acad. Sci. U.S.A. , vol.54 , pp. 1133-1141
    • Tipper, D.J.1    Strominger, J.L.2
  • 7
    • 0025052434 scopus 로고
    • Unusual septum formation in Streptococcus pneumoniae mutants with an alteration in the D,D-carboxypeptidase penicillin-binding protein 3
    • Schuster, C., Dobrinski, B., and Hakenbeck, R. (1990) Unusual septum formation in Streptococcus pneumoniae mutants with an alteration in the D,D-carboxypeptidase penicillin-binding protein 3, J. Bacteriol. 172, 6499-6505.
    • (1990) J. Bacteriol. , vol.172 , pp. 6499-6505
    • Schuster, C.1    Dobrinski, B.2    Hakenbeck, R.3
  • 8
    • 0034006505 scopus 로고    scopus 로고
    • Penicillin binding protein 5 affects cell diameter, contour, and morphology of Escherichia coli
    • Nelson, D. E., and Young, K. D. (2000) Penicillin binding protein 5 affects cell diameter, contour, and morphology of Escherichia coli, J. Bacteriol. 182, 1714-1721.
    • (2000) J. Bacteriol. , vol.182 , pp. 1714-1721
    • Nelson, D.E.1    Young, K.D.2
  • 9
    • 0346850578 scopus 로고    scopus 로고
    • Neisseria gonorrhoeae penicillin-binding protein 3 exhibits exceptionally high carboxypeptidase and β-lactam binding activities
    • Stefanova, M. E., Tomberg, J., Olesky, M., Holtje, J. V., Gutheil, W. G., and Nicholas, R. A. (2003) Neisseria gonorrhoeae penicillin-binding protein 3 exhibits exceptionally high carboxypeptidase and β-lactam binding activities, Biochemistry 42, 14614-14625.
    • (2003) Biochemistry , vol.42 , pp. 14614-14625
    • Stefanova, M.E.1    Tomberg, J.2    Olesky, M.3    Holtje, J.V.4    Gutheil, W.G.5    Nicholas, R.A.6
  • 11
    • 0034595512 scopus 로고    scopus 로고
    • The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: Implication in drug resistance
    • Gordon, E., Mouz, N., Duee, E., and Dideberg, O. (2000) The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: Implication in drug resistance, J. Mol. Biol. 299, 477-485.
    • (2000) J. Mol. Biol. , vol.299 , pp. 477-485
    • Gordon, E.1    Mouz, N.2    Duee, E.3    Dideberg, O.4
  • 12
    • 0035808477 scopus 로고    scopus 로고
    • Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-Å resolution
    • Davies, C., White, S. W., and Nicholas, R. A. (2001) Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-Å resolution, J. Biol. Chem. 276, 616-623.
    • (2001) J. Biol. Chem. , vol.276 , pp. 616-623
    • Davies, C.1    White, S.W.2    Nicholas, R.A.3
  • 13
    • 0036829003 scopus 로고    scopus 로고
    • Structural basis for the β lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus
    • Lim, D., and Strynadka, N. C. (2002) Structural basis for the β lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus, Nat. Struct. Biol. 9, 870-876.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 870-876
    • Lim, D.1    Strynadka, N.C.2
  • 14
    • 0033618429 scopus 로고    scopus 로고
    • The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15
    • Fonze, E., Vermeire, M., Nguyen-Disteche, M., Brasseur, R., and Charlier, P. (1999) The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15, J. Biol. Chem. 274, 21853-21860.
    • (1999) J. Biol. Chem. , vol.274 , pp. 21853-21860
    • Fonze, E.1    Vermeire, M.2    Nguyen-Disteche, M.3    Brasseur, R.4    Charlier, P.5
  • 15
    • 0037013989 scopus 로고    scopus 로고
    • pH, inhibitor, and substrate specificity studies on Escherichia coli penicillin-binding protein 5
    • Stefanova, M. E., Davies, C., Nicholas, R. A., and Gutheil, W. G. (2002) pH, inhibitor, and substrate specificity studies on Escherichia coli penicillin-binding protein 5, Biochim. Biophys. Acta 1597, 292-300.
    • (2002) Biochim. Biophys. Acta , vol.1597 , pp. 292-300
    • Stefanova, M.E.1    Davies, C.2    Nicholas, R.A.3    Gutheil, W.G.4
  • 16
    • 0032985224 scopus 로고    scopus 로고
    • Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: Viability, characteristics, and implications for peptidoglycan synthesis
    • Denome, S. A., Elf, P. K., Henderson, T. A., Nelson, D. E., and Young, K. D. (1999) Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: Viability, characteristics, and implications for peptidoglycan synthesis, J. Bacteriol. 181, 3981-3993.
    • (1999) J. Bacteriol. , vol.181 , pp. 3981-3993
    • Denome, S.A.1    Elf, P.K.2    Henderson, T.A.3    Nelson, D.E.4    Young, K.D.5
  • 17
    • 0035026549 scopus 로고    scopus 로고
    • Contributions of PBP 5 and DD-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli
    • Nelson, D. E., and Young, K. D. (2001) Contributions of PBP 5 and DD-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli, J. Bacteriol. 183, 3055-3064.
    • (2001) J. Bacteriol. , vol.183 , pp. 3055-3064
    • Nelson, D.E.1    Young, K.D.2
  • 18
    • 0347362788 scopus 로고    scopus 로고
    • Crystal structure of wild-type penicillin-binding protein 5 from E. coli: Implications for deacylation of the acyl-enzyme complex
    • Nicholas, R. A., Krings, S., Tomberg, J., Nicola, G., and Davies, C. (2003) Crystal structure of wild-type penicillin-binding protein 5 from E. coli: Implications for deacylation of the acyl-enzyme complex, J. Biol. Chem. 278, 52826-52833.
    • (2003) J. Biol. Chem. , vol.278 , pp. 52826-52833
    • Nicholas, R.A.1    Krings, S.2    Tomberg, J.3    Nicola, G.4    Davies, C.5
  • 19
    • 0015236369 scopus 로고
    • 2-Phenylethaneboronic acid, a possible transition-state analog for chymotrypsin
    • Koehler, K. A., and Lienhard, G. E. (1971) 2-Phenylethaneboronic acid, a possible transition-state analog for chymotrypsin, Biochemistry 10, 2477-2483.
    • (1971) Biochemistry , vol.10 , pp. 2477-2483
    • Koehler, K.A.1    Lienhard, G.E.2
  • 20
    • 0031688282 scopus 로고    scopus 로고
    • Enzymatic transition states and transition state analog design
    • Schramm, V. L. (1998) Enzymatic transition states and transition state analog design, Annu. Rev. Biochem. 67, 693-720.
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 693-720
    • Schramm, V.L.1
  • 21
    • 0033136041 scopus 로고    scopus 로고
    • Conformational aspects of inhibitor design: Enzyme-substrate interactions in the transition state
    • Wolfenden, R. (1999) Conformational aspects of inhibitor design: Enzyme-substrate interactions in the transition state, Bioorg. Med. Chem. 7, 647-652.
    • (1999) Bioorg. Med. Chem. , vol.7 , pp. 647-652
    • Wolfenden, R.1
  • 22
    • 33845556998 scopus 로고
    • R-1-Acetamido-2-phenylethaneboronic acid. A specific transition-state analog for chymotrypsin
    • Matteson, D. S., Sadhu, K. M., and Lienhard, G. E. (1981) R-1-Acetamido-2-phenylethaneboronic acid. A specific transition-state analog for chymotrypsin, J. Am. Chem. Soc. 103, 5241-5242.
    • (1981) J. Am. Chem. Soc. , vol.103 , pp. 5241-5242
    • Matteson, D.S.1    Sadhu, K.M.2    Lienhard, G.E.3
  • 23
    • 0023772989 scopus 로고
    • Kinetic properties of the binding of α-lytic protease to peptide boronic acids
    • Kettner, C. A., Bone, R., Agard, D. A., and Bachovchin, W. W. (1988) Kinetic properties of the binding of α-lytic protease to peptide boronic acids, Biochemistry 27, 7682-7688.
    • (1988) Biochemistry , vol.27 , pp. 7682-7688
    • Kettner, C.A.1    Bone, R.2    Agard, D.A.3    Bachovchin, W.W.4
  • 24
    • 0021723091 scopus 로고
    • Inhibition of the serine proteases leukocyte elastase, pancreatic elastase, cathepsin G, and chymotrypsin by peptide boronic acids
    • Kettner, C. A., and Shenvi, A. B. (1984) Inhibition of the serine proteases leukocyte elastase, pancreatic elastase, cathepsin G, and chymotrypsin by peptide boronic acids, J. Biol. Chem. 259, 15106-15114.
    • (1984) J. Biol. Chem. , vol.259 , pp. 15106-15114
    • Kettner, C.A.1    Shenvi, A.B.2
  • 25
    • 0027305358 scopus 로고
    • Separation of L-Pro-DL-boroPro into its component diastereomers and kinetic analysis of their inhibition of dipeptidyl peptidase IV. A new method for the analysis of slow, tight-binding inhibition
    • Gutheil, W. G., and Bachovchin, W. W. (1993) Separation of L-Pro-DL-boroPro into its component diastereomers and kinetic analysis of their inhibition of dipeptidyl peptidase IV. A new method for the analysis of slow, tight-binding inhibition, Biochemistry 32, 8723-8731.
    • (1993) Biochemistry , vol.32 , pp. 8723-8731
    • Gutheil, W.G.1    Bachovchin, W.W.2
  • 27
    • 0023892521 scopus 로고
    • β-lactamase inhibitors. The inhibition of serine β-lactamases by specific boronic acids
    • Crompton, I. E., Cuthbert, B. K., Lowe, G., and Waley, S. G. (1988) β-Lactamase inhibitors. The inhibition of serine β-lactamases by specific boronic acids, Biochem. J. 251, 453-459.
    • (1988) Biochem. J. , vol.251 , pp. 453-459
    • Crompton, I.E.1    Cuthbert, B.K.2    Lowe, G.3    Waley, S.G.4
  • 29
    • 0034625157 scopus 로고    scopus 로고
    • Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 β-lactamase
    • Ness, S., Martin, R., Kindler, A. M., Paetzel, M., Gold, M., Jensen, S. E., Jones, J. B., and Strynadka, N. C. (2000) Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 β-lactamase, Biochemistry 39, 5312-5321.
    • (2000) Biochemistry , vol.39 , pp. 5312-5321
    • Ness, S.1    Martin, R.2    Kindler, A.M.3    Paetzel, M.4    Gold, M.5    Jensen, S.E.6    Jones, J.B.7    Strynadka, N.C.8
  • 30
    • 0345102428 scopus 로고    scopus 로고
    • The complexed structure and antimicrobial activity of a non-β-lactam inhibitor of AmpC β-lactamase
    • Powers, R. A., Blazquez, J., Weston, G. S., Morosini, M. I., Baquero, F., and Shoichet, B. (1999) The complexed structure and antimicrobial activity of a non-β-lactam inhibitor of AmpC β-lactamase, Protein Sci. 8, 2330-2337.
    • (1999) Protein Sci. , vol.8 , pp. 2330-2337
    • Powers, R.A.1    Blazquez, J.2    Weston, G.S.3    Morosini, M.I.4    Baquero, F.5    Shoichet, B.6
  • 31
    • 0037457830 scopus 로고    scopus 로고
    • Potential transition state analogue inhibitors for the penicillin-binding proteins
    • Pechenov, A., Stefanova, M. E., Nicholas, R. A., Peddi, S., and Gutheil, W. G. (2003) Potential transition state analogue inhibitors for the penicillin-binding proteins, Biochemistry 42, 579-588.
    • (2003) Biochemistry , vol.42 , pp. 579-588
    • Pechenov, A.1    Stefanova, M.E.2    Nicholas, R.A.3    Peddi, S.4    Gutheil, W.G.5
  • 32
    • 0033593558 scopus 로고    scopus 로고
    • Synthesis of 9-fluorenylmethyl esters using 9- fluorenylmethylchloroformate
    • Merette, S. A. M., Burd, A. P., and Deadman, J. J. (1999) Synthesis of 9-fluorenylmethyl esters using 9-fluorenylmethylchloroformate, Tetrahedron Lett. 40, 753-754.
    • (1999) Tetrahedron Lett. , vol.40 , pp. 753-754
    • Merette, S.A.M.1    Burd, A.P.2    Deadman, J.J.3
  • 33
    • 0034672342 scopus 로고    scopus 로고
    • Fluorescent coupled enzyme assays for D-alanine: Application to penicillin-binding protein and vancomycin activity assays
    • Gutheil, W. G., Stefanova, M. E., and Nicholas, R. A. (2000) Fluorescent coupled enzyme assays for D-alanine: Application to penicillin-binding protein and vancomycin activity assays, Anal. Biochem. 287, 196-202.
    • (2000) Anal. Biochem. , vol.287 , pp. 196-202
    • Gutheil, W.G.1    Stefanova, M.E.2    Nicholas, R.A.3
  • 34
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 36
    • 84889120137 scopus 로고
    • Improved methods for building protein structures 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 structures in electron-density maps and the location of errors in these models, Acta Crystallogr., Sect. A 47, 110-119.
    • (1991) Acta Crystallogr., Sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.-Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 37
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr., Sect. D 53, 240-255.
    • (1997) Acta Crystallogr., Sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 38
    • 0002683145 scopus 로고
    • Bacterial enzymes interacting with β-lactam antibiotics
    • Georgopapadakou, N., and Sykes, R. B. (1983) Bacterial enzymes interacting with β-lactam antibiotics, Handb. Exp. Pharmacol. 67, 1-77.
    • (1983) Handb. Exp. Pharmacol. , vol.67 , pp. 1-77
    • Georgopapadakou, N.1    Sykes, R.B.2
  • 40
    • 0026801518 scopus 로고
    • Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution
    • Strynadka, N. C., Adachi, H., Jensen, S. E., Johns, K., Sielecki, A., Betzel, C., Sutoh, K., and James, M. N. (1992) Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution, Nature 359, 700-705.
    • (1992) Nature , vol.359 , pp. 700-705
    • Strynadka, N.C.1    Adachi, H.2    Jensen, S.E.3    Johns, K.4    Sielecki, A.5    Betzel, C.6    Sutoh, K.7    James, M.N.8
  • 41
    • 0034327676 scopus 로고    scopus 로고
    • Crystal structures of substrate and inhibitor complexes with AmpC β-lactamase: Possible implications for substrate-assisted catalysis
    • Patera, A., Blaszczak, L., and Shoichet, B. (2000) Crystal structures of substrate and inhibitor complexes with AmpC β-lactamase: Possible implications for substrate-assisted catalysis, J. Am. Chem. Soc. 122, 10504-10512.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10504-10512
    • Patera, A.1    Blaszczak, L.2    Shoichet, B.3
  • 42
    • 0023878451 scopus 로고
    • Site-directed mutants of a soluble form of penicillin-binding protein 5 from Escherichia coli and their catalytic properties
    • Nicholas, R. A., and Strominger, J. L. (1988) Site-directed mutants of a soluble form of penicillin-binding protein 5 from Escherichia coli and their catalytic properties, J. Biol. Chem. 263, 2034-2040.
    • (1988) J. Biol. Chem. , vol.263 , pp. 2034-2040
    • Nicholas, R.A.1    Strominger, J.L.2
  • 43
    • 0037432016 scopus 로고    scopus 로고
    • The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state
    • Silvaggi, N. R., Anderson, J. W., Brinsmade, S. R., Pratt, R. F., and Kelly, J. A. (2003) The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state, Biochemistry 42, 1199-1208.
    • (2003) Biochemistry , vol.42 , pp. 1199-1208
    • Silvaggi, N.R.1    Anderson, J.W.2    Brinsmade, S.R.3    Pratt, R.F.4    Kelly, J.A.5
  • 44
    • 0042068160 scopus 로고    scopus 로고
    • On the substrate specificity of bacterial DD-peptidases: Evidence from two series of peptidoglycan-mimetic peptides
    • Anderson, J. W., Adediran, S. A., Charlier, P., Nguyen-Disteche, M., Frere, J. M., Nicholas, R. A., and Pratt, R. F. (2003) On the substrate specificity of bacterial DD-peptidases: Evidence from two series of peptidoglycan-mimetic peptides, Biochem. J. 373, 949-955.
    • (2003) Biochem. J. , vol.373 , pp. 949-955
    • Anderson, J.W.1    Adediran, S.A.2    Charlier, P.3    Nguyen-Disteche, M.4    Frere, J.M.5    Nicholas, R.A.6    Pratt, R.F.7
  • 45
    • 0034633999 scopus 로고    scopus 로고
    • Dipeptide binding to the extended active site of the Streptomyces R61 D-alanyl-D-alanine-peptidase: The path to a specific substrate
    • Anderson, J. W., and Pratt, J. M. (2000) Dipeptide binding to the extended active site of the Streptomyces R61 D-alanyl-D-alanine-peptidase: The path to a specific substrate, Biochemistry 39, 12200-12209.
    • (2000) Biochemistry , vol.39 , pp. 12200-12209
    • Anderson, J.W.1    Pratt, J.M.2
  • 46
    • 0026778555 scopus 로고
    • Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding
    • Malhotra, K. T., and Nicholas, R. A. (1992) Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding, J. Biol. Chem. 267, 11386-11391.
    • (1992) J. Biol. Chem. , vol.267 , pp. 11386-11391
    • Malhotra, K.T.1    Nicholas, R.A.2
  • 47
    • 0030883194 scopus 로고    scopus 로고
    • Nuances of mechanisms and their implications for evolution of the versatile β-lactamase activity: From biosynthetic enzymes to drug resistance factors
    • Bulychev, A., Massova, I., Miyashita, K., and Mobashery, S. (1997) Nuances of mechanisms and their implications for evolution of the versatile β-lactamase activity: From biosynthetic enzymes to drug resistance factors, J. Am. Chem. Soc. 119, 7619-7625.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 7619-7625
    • Bulychev, A.1    Massova, I.2    Miyashita, K.3    Mobashery, S.4


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