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Volumn 80, Issue 3, 2012, Pages 722-732

Crystal structure of bacteriophage φNIT1 zinc peptidase PghP that hydrolyzes γ-glutamyl linkage of bacterial poly-γ-glutamate

Author keywords

Bacillus subtilis bacteriophage; Merohedral twin; Metallopeptidase; Poly glutamate hydrolase; Zinc ion

Indexed keywords

BACTERIAL ENZYME; GAMMA GLUTAMYL HYDROLASE; GLUTAMIC ACID; METALLOPROTEINASE; POLYGAMMA GLUTAMATE HYDROLASE P; UNCLASSIFIED DRUG; ZINC BINDING PROTEIN; ZINC ION;

EID: 84856804738     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23229     Document Type: Article
Times cited : (9)

References (59)
  • 2
  • 3
    • 77149154385 scopus 로고    scopus 로고
    • Matrix metalloproteinases: Fold and function of their catalytic domains
    • Tallant C, Marrero A, Gomis-Ruth FX. Matrix metalloproteinases: Fold and function of their catalytic domains. Biochim Biophys Acta 2010; 1803: 20-28.
    • (2010) Biochim Biophys Acta , vol.1803 , pp. 20-28
    • Tallant, C.1    Marrero, A.2    Gomis-Ruth, F.X.3
  • 4
    • 0037545836 scopus 로고    scopus 로고
    • Characterization of poly-gamma-glutamate hydrolase encoded by a bacteriophage genome: possible role in phage infection of Bacillus subtilis encapsulated with poly-gamma-glutamate
    • Kimura K, Itoh Y. Characterization of poly-gamma-glutamate hydrolase encoded by a bacteriophage genome: possible role in phage infection of Bacillus subtilis encapsulated with poly-gamma-glutamate. Appl Environ Microbiol 2003; 69: 2491-2497.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 2491-2497
    • Kimura, K.1    Itoh, Y.2
  • 5
    • 67049155609 scopus 로고    scopus 로고
    • Expression of the pgsB encoding the poly-gamma-DL-glutamate synthetase of Bacillus subtilis (natto)
    • Kimura K, Tran LS, Do TH, Itoh Y. Expression of the pgsB encoding the poly-gamma-DL-glutamate synthetase of Bacillus subtilis (natto). Biosci Biotech Biochem 2009; 73: 1149-1155.
    • (2009) Biosci Biotech Biochem , vol.73 , pp. 1149-1155
    • Kimura, K.1    Tran, L.S.2    Do, T.H.3    Itoh, Y.4
  • 6
    • 33745289074 scopus 로고    scopus 로고
    • Poly-gamma-glutamate in bacteria
    • Candela T, Fouet A. Poly-gamma-glutamate in bacteria. Mol Microbiol 2006; 60: 1091-1098.
    • (2006) Mol Microbiol , vol.60 , pp. 1091-1098
    • Candela, T.1    Fouet, A.2
  • 7
    • 22644436621 scopus 로고    scopus 로고
    • Bacillus anthracis CapD, belonging to the gamma-glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan
    • Candela T, Fouet A. Bacillus anthracis CapD, belonging to the gamma-glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan. Mol Microbiol 2005; 57: 717-726.
    • (2005) Mol Microbiol , vol.57 , pp. 717-726
    • Candela, T.1    Fouet, A.2
  • 8
    • 11044230062 scopus 로고    scopus 로고
    • Characterization of Bacillus subtilis gamma-glutamyltransferase and its involvement in the degradation of capsule poly-gamma-glutamate
    • Kimura K, Tran LS, Uchida I, Itoh Y. Characterization of Bacillus subtilis gamma-glutamyltransferase and its involvement in the degradation of capsule poly-gamma-glutamate. Microbiology 2004; 150: 4115-4123.
    • (2004) Microbiology , vol.150 , pp. 4115-4123
    • Kimura, K.1    Tran, L.S.2    Uchida, I.3    Itoh, Y.4
  • 9
    • 34548409520 scopus 로고    scopus 로고
    • Genetic design of conditional D-glutamate auxotrophy for Bacillus subtilis: use of a vector-borne poly-gamma-glutamate synthetic system
    • Ashiuchi M, Nishikawa Y, Matsunaga K, Yamamoto M, Shimanouchi K, Misono H. Genetic design of conditional D-glutamate auxotrophy for Bacillus subtilis: use of a vector-borne poly-gamma-glutamate synthetic system. Biochem Biophys Res Commun 2007; 362: 646-650.
    • (2007) Biochem Biophys Res Commun , vol.362 , pp. 646-650
    • Ashiuchi, M.1    Nishikawa, Y.2    Matsunaga, K.3    Yamamoto, M.4    Shimanouchi, K.5    Misono, H.6
  • 10
    • 14644386821 scopus 로고    scopus 로고
    • Key role of poly-gamma-DL-glutamic acid in immune evasion and virulence of Staphylococcus epidermidis
    • Kocianova S, Vuong C, Yao Y, Voyich JM, Fischer ER, DeLeo FR, Otto M. Key role of poly-gamma-DL-glutamic acid in immune evasion and virulence of Staphylococcus epidermidis. J Clin Invest 2005; 115: 688-694.
    • (2005) J Clin Invest , vol.115 , pp. 688-694
    • Kocianova, S.1    Vuong, C.2    Yao, Y.3    Voyich, J.M.4    Fischer, E.R.5    DeLeo, F.R.6    Otto, M.7
  • 11
    • 0027250038 scopus 로고
    • Identification of a novel gene, dep, associated with depolymerization of the capsular polymer in Bacillus anthracis
    • Uchida I, Makino S, Sasakawa C, Yoshikawa M, Sugimoto C, Terakado N. Identification of a novel gene, dep, associated with depolymerization of the capsular polymer in Bacillus anthracis. Mol Microbiol 1993; 9: 487-496.
    • (1993) Mol Microbiol , vol.9 , pp. 487-496
    • Uchida, I.1    Makino, S.2    Sasakawa, C.3    Yoshikawa, M.4    Sugimoto, C.5    Terakado, N.6
  • 12
    • 0012516577 scopus 로고
    • A new species (Flavobacterium polyglutamicum) which hydrolyzes the gamma-L-glutamyl bond in polypeptides
    • Volcani BE, Margalith P. A new species (Flavobacterium polyglutamicum) which hydrolyzes the gamma-L-glutamyl bond in polypeptides. J Bacteriol 1957; 74: 646-655.
    • (1957) J Bacteriol , vol.74 , pp. 646-655
    • Volcani, B.E.1    Margalith, P.2
  • 13
    • 85007856438 scopus 로고
    • Purification and characterization of poly(γ-glutamic acid) hydrolase from a filamentous fungus, Myrothecium sp. TM-4222
    • Tanaka T, Hiruta O, Futamura T, Uotani K, Satoh A, Taniguchi M, Oi S. Purification and characterization of poly(γ-glutamic acid) hydrolase from a filamentous fungus, Myrothecium sp. TM-4222. Biosci Biotech Biochem 1993; 57: 2148-2153.
    • (1993) Biosci Biotech Biochem , vol.57 , pp. 2148-2153
    • Tanaka, T.1    Hiruta, O.2    Futamura, T.3    Uotani, K.4    Satoh, A.5    Taniguchi, M.6    Oi, S.7
  • 14
    • 85004571497 scopus 로고
    • Screening for microorganisms having poly(γ-glutamic acid) endohydrolase activity and the enzyme production by Myrothecium sp. TM-4222
    • Tanaka T, Yaguchi T, Hiruta O, Futamura T, Uotani K, Satoh A, Taniguchi M, Oi S. Screening for microorganisms having poly(γ-glutamic acid) endohydrolase activity and the enzyme production by Myrothecium sp. TM-4222. Biosci Biotech Biochem 1993; 57: 1809-1810.
    • (1993) Biosci Biotech Biochem , vol.57 , pp. 1809-1810
    • Tanaka, T.1    Yaguchi, T.2    Hiruta, O.3    Futamura, T.4    Uotani, K.5    Satoh, A.6    Taniguchi, M.7    Oi, S.8
  • 15
    • 84856796707 scopus 로고    scopus 로고
    • Enzymatic degradation of poly-gamma-glutamic acid
    • Hamano Y, editor. Heidelberg: Springer;
    • Kimura K, Fujimoto Z. Enzymatic degradation of poly-gamma-glutamic acid. In: Hamano Y, editor. Amino-Acid Homopolymers Occurring in Nature. Heidelberg: Springer; 2010. p 95-117.
    • (2010) Amino-Acid Homopolymers Occurring in Nature , pp. 95-117
    • Kimura, K.1    Fujimoto, Z.2
  • 16
    • 58449083093 scopus 로고    scopus 로고
    • Macrophage uptake, intracellular localization, and degradation of poly-gamma-D-glutamic acid, the capsular antigen of Bacillus anthracis
    • Sutherland MD, Kozel TR. Macrophage uptake, intracellular localization, and degradation of poly-gamma-D-glutamic acid, the capsular antigen of Bacillus anthracis. Infect Immun 2009; 77: 532-538.
    • (2009) Infect Immun , vol.77 , pp. 532-538
    • Sutherland, M.D.1    Kozel, T.R.2
  • 18
    • 69849087548 scopus 로고    scopus 로고
    • Crystallization and preliminary crystallographic analysis of poly-γ-glutamate hydrolase from bacteriophage ΦNIT1
    • Fujimoto Z, Shiga I, Itoh Y, Kimura K. Crystallization and preliminary crystallographic analysis of poly-γ-glutamate hydrolase from bacteriophage ΦNIT1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65: 913-916.
    • (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun , vol.65 , pp. 913-916
    • Fujimoto, Z.1    Shiga, I.2    Itoh, Y.3    Kimura, K.4
  • 19
    • 0022273106 scopus 로고
    • 15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type
    • 15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 1985; 24: 7263-7268.
    • (1985) Biochemistry , vol.24 , pp. 7263-7268
    • LeMaster, D.M.1    Richards, F.M.2
  • 20
    • 0031045585 scopus 로고    scopus 로고
    • Preparation of selenomethionyl proteins for phase determination
    • Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol 1997; 276: 523-530.
    • (1997) Methods Enzymol , vol.276 , pp. 523-530
    • Doublie, S.1
  • 21
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997; 276: 307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 22
    • 0036848846 scopus 로고    scopus 로고
    • Automated structure solution, density modification and model building
    • Terwilliger TC. Automated structure solution, density modification and model building. Acta Crystallogr D Biol Crystallogr 2002; 58: 1937-1940.
    • (2002) Acta Crystallogr D Biol Crystallogr , vol.58 , pp. 1937-1940
    • Terwilliger, T.C.1
  • 24
  • 26
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • Collaborative Computational Project N
    • Collaborative Computational Project N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994; 50: 760-763.
    • (1994) Acta Crystallogr D Biol Crystallogr , vol.50 , pp. 760-763
  • 27
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A, Teplyakov A. MOLREP: an automated program for molecular replacement. J Appl Crystallogr 1997; 30: 1022-1025.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 29
    • 0037779022 scopus 로고    scopus 로고
    • A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning
    • Padilla JE, Yeates TO. A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr D Biol Crystallogr 2003; 59: 1124-1130.
    • (2003) Acta Crystallogr D Biol Crystallogr , vol.59 , pp. 1124-1130
    • Padilla, J.E.1    Yeates, T.O.2
  • 32
  • 34
    • 0026243741 scopus 로고
    • Atomic accessible and contact surfaces as restraints in the Hendrickson & Konnert refinement program
    • Kraulis PJ. Atomic accessible and contact surfaces as restraints in the Hendrickson & Konnert refinement program. J Appl Crystallogr 1991; 24: 946-950.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 35
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D photorealistic molecular graphics
    • Merritt EA, Bacon DJ. Raster3D photorealistic molecular graphics. Methods Enzymol 1997; 277: 505-524.
    • (1997) Methods Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 36
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews BW. Solvent content of protein crystals. J Mol Biol 1968; 33: 491-497.
    • (1968) J Mol Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 38
    • 34548361744 scopus 로고    scopus 로고
    • An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer
    • MacRae IJ, Doudna JA. An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer. Acta Crystallogr D Biol Crystallogr 2007; 63: 993-999.
    • (2007) Acta Crystallogr D Biol Crystallogr , vol.63 , pp. 993-999
    • MacRae, I.J.1    Doudna, J.A.2
  • 39
    • 0018892931 scopus 로고
    • Structure of potato inhibitor complex of carboxypeptidase A at 5.5-Å resolution
    • Rees DC, Lipscomb WN. Structure of potato inhibitor complex of carboxypeptidase A at 5.5-Å resolution. Proc Natl Acad Sci USA 1980; 77: 277-280.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 277-280
    • Rees, D.C.1    Lipscomb, W.N.2
  • 40
    • 0032189646 scopus 로고    scopus 로고
    • Dictionary of recurrent domains in protein structures
    • Holm L, Sander C. Dictionary of recurrent domains in protein structures. Proteins Struct Funct Bioinf 1998; 33: 88-96.
    • (1998) Proteins Struct Funct Bioinf , vol.33 , pp. 88-96
    • Holm, L.1    Sander, C.2
  • 41
    • 0014942119 scopus 로고
    • The structure of carboxypeptidase A. 8. Atomic interpretation at 0.2 nm resolution, a new study of the complex of glycyl-L-tyrosine with CPA, and mechanistic deductions
    • Lipscomb WN, Reeke GN, Jr., Hartsuck JA, Quiocho FA, Bethge PH. The structure of carboxypeptidase A. 8. Atomic interpretation at 0.2 nm resolution, a new study of the complex of glycyl-L-tyrosine with CPA, and mechanistic deductions. Philos Trans R Soc Lond B Biol Sci 1970; 257: 177-214.
    • (1970) Philos Trans R Soc Lond B Biol Sci , vol.257 , pp. 177-214
    • Lipscomb, W.N.1    Reeke Jr, G.N.2    Hartsuck, J.A.3    Quiocho, F.A.4    Bethge, P.H.5
  • 42
    • 0026673902 scopus 로고
    • Structural comparison of sulfodiimine and sulfonamide inhibitors in their complexes with zinc enzymes
    • Cappalonga AM, Alexander RS, Christianson DW. Structural comparison of sulfodiimine and sulfonamide inhibitors in their complexes with zinc enzymes. J Biol Chem 1992; 267: 19192-19197.
    • (1992) J Biol Chem , vol.267 , pp. 19192-19197
    • Cappalonga, A.M.1    Alexander, R.S.2    Christianson, D.W.3
  • 46
    • 0035844274 scopus 로고    scopus 로고
    • The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases
    • Aloy P, Companys V, Vendrell J, Aviles FX, Fricker LD, Coll M, Gomis-Ruth FX. The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases. J Biol Chem 2001; 276: 16177-16184.
    • (2001) J Biol Chem , vol.276 , pp. 16177-16184
    • Aloy, P.1    Companys, V.2    Vendrell, J.3    Aviles, F.X.4    Fricker, L.D.5    Coll, M.6    Gomis-Ruth, F.X.7
  • 47
    • 0025316455 scopus 로고
    • Catalytic and conformational changes induced by limited subtilisin cleavage of bovine carboxypeptidase A
    • Solomon BM, Larsen KS, Riordan JF. Catalytic and conformational changes induced by limited subtilisin cleavage of bovine carboxypeptidase A. Biochemistry 1990; 29: 7303-7309.
    • (1990) Biochemistry , vol.29 , pp. 7303-7309
    • Solomon, B.M.1    Larsen, K.S.2    Riordan, J.F.3
  • 48
    • 0026409452 scopus 로고
    • Structural biology of zinc
    • Christianson DW. Structural biology of zinc. Adv Protein Chem 1991; 42: 281-355.
    • (1991) Adv Protein Chem , vol.42 , pp. 281-355
    • Christianson, D.W.1
  • 49
    • 67650504166 scopus 로고    scopus 로고
    • Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism
    • Xu D, Guo H. Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism. J Am Chem Soc 2009; 131: 9780-9788.
    • (2009) J Am Chem Soc , vol.131 , pp. 9780-9788
    • Xu, D.1    Guo, H.2
  • 50
    • 0022137161 scopus 로고
    • Binding of a possible transition state analogue to the active site of carboxypeptidase A
    • Christianson DW, Lipscomb WN. Binding of a possible transition state analogue to the active site of carboxypeptidase A. Proc Natl Acad Sci USA 1985; 82: 6840-6844.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 6840-6844
    • Christianson, D.W.1    Lipscomb, W.N.2
  • 51
    • 0000437149 scopus 로고
    • X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature
    • Christianson DW, Lipscomb WN. X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature. Proc Natl Acad Sci USA 1986; 83: 7568-7572.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 7568-7572
    • Christianson, D.W.1    Lipscomb, W.N.2
  • 52
    • 0023424963 scopus 로고
    • Purification and properties of formylglutamate amidohydrolase from Pseudomonas putida
    • Hu L, Mulfinger LM, Phillips AT. Purification and properties of formylglutamate amidohydrolase from Pseudomonas putida. J Bacteriol 1987; 169: 4696-4702.
    • (1987) J Bacteriol , vol.169 , pp. 4696-4702
    • Hu, L.1    Mulfinger, L.M.2    Phillips, A.T.3
  • 54
    • 0024375849 scopus 로고
    • Phosphonate analogues of carboxypeptidase A substrates are potent transition-state analogue inhibitors
    • Hanson JE, Kaplan AP, Bartlett PA. Phosphonate analogues of carboxypeptidase A substrates are potent transition-state analogue inhibitors. Biochemistry 1989; 28: 6294-6305.
    • (1989) Biochemistry , vol.28 , pp. 6294-6305
    • Hanson, J.E.1    Kaplan, A.P.2    Bartlett, P.A.3
  • 55
    • 0025333937 scopus 로고
    • Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes
    • Kim H, Lipscomb WN. Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes. Biochemistry 1990; 29: 5546-5555.
    • (1990) Biochemistry , vol.29 , pp. 5546-5555
    • Kim, H.1    Lipscomb, W.N.2
  • 56
    • 0025938822 scopus 로고
    • Comparison of the structures of three carboxypeptidase A-phosphonate complexes determined by X-ray crystallography
    • Kim H, Lipscomb WN. Comparison of the structures of three carboxypeptidase A-phosphonate complexes determined by X-ray crystallography. Biochemistry 1991; 30: 8171-8180.
    • (1991) Biochemistry , vol.30 , pp. 8171-8180
    • Kim, H.1    Lipscomb, W.N.2
  • 57
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876-4882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 58
    • 24944566164 scopus 로고    scopus 로고
    • Gamma-Glutamyl transpeptidase and its precursor
    • Barrett AJ,Rawlings ND,Woessner JF, editors.,2nd ed. London: Elsevier
    • Hiratake J, Suzuki H, Kumagai H. Gamma-Glutamyl transpeptidase and its precursor. In: Barrett AJ, Rawlings ND, Woessner JF, editors. Handbook of Proteolytic Enzymes, 2nd ed. London: Elsevier; 2004. p 2090-2094.
    • (2004) Handbook of Proteolytic Enzymes , pp. 2090-2094
    • Hiratake, J.1    Suzuki, H.2    Kumagai, H.3


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