Structural modelling of substrate binding and inhibition in penicillin V acylase from Pectobacterium atrosepticum

Biochemical and Biophysical Research Communications

Volumn 437, Issue 4, 2013, Pages 538-543

  Avinash, V S ^a   Panigrahi, Priyabrata ^a   Suresh, C G ^a   Pundle, Archana V ^a   Ramasamy, Sureshkumar ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

Bile salt hydrolase; Docking; Homology modelling; Inhibition; Pectobacterium; Penicillin acylase

Indexed keywords

BILE SALT HYDROLASE; HYDROLASE; PENICILLIN V; PENICILLIN V ACRYLASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INHIBITION; ENZYME SPECIFICITY; ENZYME STRUCTURE; HYDROLYSIS; MOLECULAR DOCKING; NONHUMAN; PECTOBACTERIUM; PECTOBACTERIUM ATROSEPTICUM; PRIORITY JOURNAL;

BILE SALT HYDROLASE; DOCKING; HOMOLOGY MODELLING; INHIBITION; PECTOBACTERIUM; PENICILLIN ACYLASE;

AMIDOHYDROLASES; BACTERIAL PROTEINS; BILE ACIDS AND SALTS; CATALYTIC DOMAIN; DOSE-RESPONSE RELATIONSHIP, DRUG; HYDROGEN BONDING; HYDROLYSIS; MOLECULAR DOCKING SIMULATION; PECTOBACTERIUM; PENICILLIN AMIDASE; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

NEGIBACTERIA; PECTOBACTERIUM; PECTOBACTERIUM ATROSEPTICUM;

EID: 84881545880     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2013.06.109     Document Type: Article

References (28)

1. Christiaens H., Leer R.J., Pouwels P.H., Verstraete W. Cloning and expression of a conjugated bile-acid hydrolase gene from Lactobacillus plantarum by using a direct plate assay. Appl. Environ. Microbiol. 1992, 58:3792-3798.
2. Shewale J.G., Sudhakaran V.K. Penicillin V acylase: its potential in the production of 6-aminopenicillanic acid. Enzyme Microb. Technol. 1997, 20:402-410.
3. Desmet I., Vanhoorde L., Woestyne M.V., Christiaens H., Verstraete W. Significance of bile-salt hydrolytic activities of Lactobacilli. J. Appl. Bacteriol. 1995, 79:292-301.
4. Klaver F.A.M., Vandermeer R. The assumed assimilation of cholesterol by Lactobacilli and Bifidobacterium bifidum is due to their bile salt-deconjugating activity. Appl. Environ. Microbiol. 1993, 59:1120-1124.
5. Dussurget O., Cabanes D., Dehoux P., Lecuit M., Buchrieser C., Glaser P., Cossart P. Listeria monocytogenes bile salt hydrolase is a PrfA-regulated virulence factor involved in the intestinal and hepatic phases of listeriosis. Mol. Microbiol. 2002, 45:1095-1106.
6. Delpino M.V., Marchesini M.I., Estein S.M., Comerci D.J., Cassataro J., Fossati C.A., Baldi P.C. A bile salt hydrolase of Brucella abortus contributes to the establishment of a successful infection through the oral route in mice. Infect. Immun. 2007, 75:299-305.
7. Valle F., Balbas P., Merino E., Bolivar F. The role of penicillin amidases in nature and in industry. Trends Biochem. Sci. 1991, 16:36-40.
8. Kovacikova G., Lin W., Skorupski K. The virulence activator AphA links quorum sensing to pathogenesis and physiology in Vibrio cholerae by repressing the expression of a penicillin amidase gene on the small chromosome. J. Bacteriol. 2003, 185:4825-4836.
9. Kumar R.S., Brannigan J.A., Prabhune A.A., Pundle A.V., Dodson G.G., Dodson E.J., Suresh C.G. Structural and functional analysis of a conjugated bile salt hydrolase from Bifidobacterium longum reveals an evolutionary relationship with penicillin V acylase. J. Biol. Chem. 2006, 281:32516-32525.
10. Shewale G.J., Kumar K.K., Ambekar G.R. Evaluation of determination of 6-aminopenicillanic acid by p-dimethyl aminobenzaldehyde. Biotechnol. Tech. 1987, 1:69-72.
11. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 2000, 28:235-242.
12. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J.H., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
13. Prime, version 3.0, Schrodinger, LLC, New York, NY, 2011.
14. Laskowski R.A., Macarthur M.W., Moss D.S., Thornton J.M. PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
15. Eisenberg D., Luthy R., Bowie J.U. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 1997, 277:396-404.
16. Wiederstein M., Sippl M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007, 35:W407-W410.
17. E. Bolton, Y. Wang, P.A. Thiessen, S.H. Bryant, PubChem: Integrated platform of mall molecules and biological activities, in: Annual Reports in Computational Chemistry, Elsevier, Washington DC, 2008, pp. 217-241.
18. LigPrep, version 2.5, Schrodinger, LLC, New York, NY, 2012.
19. Glide, version 5.8, Schrodinger, LLC, New York, NY, 2012.
20. Begley M., Hill C., Gahan C.G.M. Bile salt hydrolase activity in probiotics. Appl. Environ. Microbiol. 2006, 72:1729-1738.
21. Suresh C.G., Pundle A.V., SivaRaman H., Rao K.N., Brannigan J.A., McVey C.E., Verma C.S., Dauter Z., Dodson E.J., Dodson G.G. Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members. Nat. Struct. Mol. Biol. 1999, 6:414-416.
22. Rathinaswamy P., Pundle A.V., Prabhune A.A., SivaRaman H., Brannigan J.A., Dodson G.G., Suresh C.G. Cloning, purification, crystallization and preliminary structural studies of penicillin V acylase from Bacillus subtilis. Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 2005, 61:680-683.
23. Rossocha M., Schultz-Heienbrok R., von Moeller H., Coleman J.P., Saenger W. Conjugated bile acid hydrolase is a tetrameric N-terminal thiol hydrolase with specific recognition of its cholyl but not of its tauryl product. Biochemistry 2005, 44:5739-5748.
24. Pundle A., SivaRaman H. Bacillus sphaericus penicillin V acylase: purification, substrate specificity, and active-site characterization. Curr. Microbiol. 1997, 34:144-148.
25. Rathinaswamy P., Gaikwad S.M., Suresh C.G., Prabhune A.A., Brannigan J.A., Dodson G.G., Pundle A.V. Purification and characterization of YxeI, a penicillin acylase from Bacillus subtilis. Int. J. Biol. Macromol. 2012, 50:25-30.
26. Lodola A., Branduardi D., De Vivo M., Capoferri L., Mor M., Piomelli D., Cavalli A. A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS One 2012, 7:e32397. 10.1371/journal.pone.0032397.
27. SiteMap, version 2.5, Schrodinger, LLC, New York, NY, 2011.
28. Lambert J.M., Bongers R.S., de Vos W.M., Kleerebezem M. Functional analysis of four bile salt hydrolase and penicillin acylase family members in Lactobacillus plantarum WCFS1. Appl. Environ. Microbiol. 2008, 74:4719-4726.