[en] The bacterial DD-peptidases or penicillin-binding proteins (PBPs) catalyze the formation and regulation of cross-links in peptidoglycan biosynthesis. They are classified into two groups, the high-molecular mass (HMM) and lowmolecular mass (LMM) enzymes. The latter group, which is subdivided into classes A−C (LMMA, -B, and -C, respectively), is believed to catalyze DD-carboxypeptidase and endopeptidase reactions in vivo. To date, the specificity of their reactions with particular elements of peptidoglycan structure has not, in general, been defined.
This paper describes the steady-state kinetics of hydrolysis of a series of specific
peptidoglycan-mimetic peptides, representing various elements of stem peptide structure, catalyzed by a range of LMM PBPs (the LMMA enzymes, Escherichia coli PBP5, Neisseria gonorrhoeae PBP4, and Streptococcus pneumoniae PBP3, and the LMMC enzymes, the Actinomadura R39 DD-peptidase, Bacillus subtilis PBP4a, and N. gonorrhoeae PBP3). The R39 enzyme (LMMC), like the previously studied Streptomyces R61 DD-peptidase (LMMB), specifically and rapidly hydrolyzes stem peptide fragments with a free N-terminus. In accord with this result, the crystal structures of the R61 and R39 enzymes display a binding site specific to the stem peptide N-terminus. These are water-soluble enzymes, however, with no known specific function in vivo. On the other hand, soluble versions of the remaining enzymes of those noted above, all of which are likely to be membrane-bound and/or associated in vivo and have been assigned particular roles in cell wall biosynthesis and maintenance, show little or no specificity for peptides containing elements of peptidoglycan structure. Peptidoglycan-mimetic boronate transition-state analogues do inhibit these enzymes but display notable specificity only for the LMMC enzymes, where, unlike peptide substrates, they may be
able to effectively induce a specific active site structure. The manner in which LMMA (and HMM) DD-peptidases achieve substrate specificity, both in vitro and in vivo, remains unknown.
Research Center/Unit :
Department of £chemistry, Wesleyan university
Disciplines :
Microbiology
Author, co-author :
Nemmara, Venkatesh V; Wesleyan university, connecticut 06459 USA > Department of Chemistry
Dzhekieva, Liudmila; Wesleyan university, connecticut 06459 USA > Department of Chemistry
Subarno Sakar, Kumar; Wesleyan University, Connecticut 06459, USA > Department of Chemistry
Adediran, S. A.; Wesleyan University, Connecticut 06459, USA > Department of Chemistry
Duez, Colette ; Université de Liège - ULiège > Centre d'ingénierie des protéines
Nicholas, Robert A.; University of North Carolina, North Carolina 27599-7365, USA > Department of Pharmacology
Pratt, Rex F.; Wesleyan University, Connecticut 06459, USA > Department of Chemistry
Language :
English
Title :
Substrate Specificity of Low-Molecular Mass Bacterial DD-Peptidases
Alternative titles :
[fr] Spécificité de substrat des DD-peptidases bactériennes de faible poids moléculaire
Publication date :
27 October 2011
Journal title :
Biochemistry
ISSN :
0006-2960
eISSN :
1520-4995
Publisher :
American Chemical Society, Washington, United States - District of Columbia
Volume :
50
Pages :
10091-10101
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
NIH - National Institutes of Health F.R.S.-FNRS - Fonds de la Recherche Scientifique BELSPO - Belgian Science Policy Office
Funding text :
This research was supported by National Institutes of Health
Grants AI-17986 (R.F.P.) and AI-36901 (R.A.N.). C.D. is
chercheur Qualifié of the fonds National de la Recherche
Scientifique (FRS-FNRS, Brussels, Belgium). The work in Liège
was supported by the Belgian Program on Interuniversity Poles of
Attraction initiated by the Belgian State, Prime Minister’s Office,
Science Policy Programming (PAI 6/19).
Höltje, J.-V. (1998) Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli Microbiol. Mol. Biol. Rev. 62, 181-203 (Pubitemid 28130800)
Vollmer, W. and Bertsche, U. (2007) Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli Biochim. Biophys. Acta 1788, 1714-1733
Joris, B. and Frère, J.-M. (1988) Penicillin-sensitive enzymes in peptidoglycan biosynthesis CRC Crit. Rev. Microbiol. 11, 299-396
Hackenbeck, R. and Coyette, J. (1998) Resistant penicillin-binding proteins Cell. Mol. Life Sci. 54, 332-340 (Pubitemid 28192739)
Barlow, M. (2009) What antimicrobial resistance has taught us about horizontal gene transfer Methods Mol. Biol. 532, 397-411
Pinho, M. G., de Lencastre, H., and Tomasz, A. (2001) An acquired and a native penicillin-binding protein cooperate in building the cell wall of drug-resistant staphylococci Proc. Natl. Acad. Sci. U.S.A. 98, 10886-10891 (Pubitemid 32878714)
Spratt, B. G. (1994) Resistance to antibiotics mediated by target alterations Science 264, 388-393 (Pubitemid 24986723)
Reinert, R. R. (2009) The antibiotic resistance profile of Streptococcus pneumoniae Clin. Microbiol. Infect. 15 (Suppl. 3) 7-11
Fontana, R., Aldegheri, M., Ligozzi, M., Lopez, H., Sucari, R., and Satta, G. (1994) Overproduction of a low-affinity penicillin-binding protein and high-level ampicillin resistance in Enterococcus faecium Antimicrob. Agents Chemother. 38, 1980-1983 (Pubitemid 24278788)
Lindberg, R., Fredlund, H., Nicholas, R., and Unemo, M. (2007) Neisseria gonorrhoeae isolates with reduced susceptibility to cefixime and ceftriaxone: Association with genetic polymorphisms in penA, mtrR, porB1b, and ponA Antimicrob. Agents Chemother. 51, 2117-2122 (Pubitemid 46903103)
Page, M. G. P. (2007) Ceftobiprole: A case study Expert Opin. Drug Discovery 2, 115-129
Shahid, M., Sobia, F., Singh, A., Malik, A., Khan, H. M., Jonas, D., and Hawkey, P. M. (2009) β-Lactams and β-lactamase inhibitors in current or potential clinical practice: A comprehensive update Crit. Rev. Microbiol. 35, 81-108
Popham, D. L. and Young, K. D. (2003) Role of penicillin-binding proteins in bacterial cell morphogenesis Curr. Opin. Microbiol. 6, 594-599 (Pubitemid 38020056)
Ghosh, A. S., Chowdhury, C., and Nelson, D. E. (2008) Physiological functions of d -alanine carboxypeptidases in Escherichia coli Trends Microbiol. 16, 309-317
Ghuysen, J.-M., Frère, J.-M., Leyh-Bouille, M., Coyette, J., Dusart, J., and Nguyen-Distèche, M. (1979) Use of model enzymes in determination of the mode of action of penicillins and Δ3-cephalosporins Annu. Rev. Biochem. 48, 73-101
Adam, M., Damblon, C., Plaitin, B., Christiaens, L., and Frère, J.-M. (1990) Chromogenic depsipeptide substrates for β-lactamases and penicillin-sensitive dd -peptidases Biochem. J. 270, 525-529 (Pubitemid 20273499)
Anderson, J. W. and Pratt, R. F. (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
McDonough, M. A., Anderson, J. W., Silvaggi, N. R., Pratt, R. F., and Kelly, J. A. (2002) Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins J. Mol. Biol. 322, 111-122 (Pubitemid 36132673)
Kumar, I. and Pratt, R. F. (2005) Transpeptidation reactions of a specific substrate catalyzed by the Streptomyces R61 dd -peptidase: The structural basis of acyl acceptor specificity Biochemistry 44, 9961-9970 (Pubitemid 41076792)
Kumar, I. and Pratt, R. F. (2005) Transpeptidation reactions of a specific substrate catalyzed by the Streptomyces R61 dd -peptidase: Characterization of a chromogenic substrate and acyl acceptor design Biochemistry 44, 9971-9979 (Pubitemid 41076793)
Rhazi, N., Delmarcelle, M., Sauvage, E., Jacquemotte, F., Devriendt, K., Tallon, V., Ghosez, L., and Frère, J.-M. (2005) Specificity and reversibility of the transpeptidation reaction catalyzed by the Streptomyces R61 d -Ala- d -Ala peptidase Protein Sci. 14, 2922-2928 (Pubitemid 41577274)
Leyh-Bouille, M., Nakel, M., Frère, J.-M., Johnson, K., Ghuysen, J.-M., Nieto, M., and Perkins, H. R. (1972) Penicillin-sensitive dd -carboxypeptidases from Streptomyces strains R39 and K11 Biochemistry 11, 1290-1298
Ghuysen, J.-M., Leyh-Bouille, M., Campbell, J. N., Moreno, R., Frère, J.-M., Duez, C., Nieto, M., and Perkins, H. R. (1973) Structure of the wall peptidoglycan of Streptomyces R39 and the specificity profile of its exocellular dd -carboxypeptidase-transpeptidase for peptide acceptors Biochemistry 12, 1243-1251
Ghuysen, J.-M., Reynolds, P. E., Perkins, H. R., Frère, J.-M., and Moreno, R. (1974) Effects of donor and acceptor peptides on concomitant hydrolysis and transfer reactions catalyzed by the exocellular dd -carboxypeptidase-transpeptidase from Streptomyces R39 Biochemistry 13, 2539-2547
Adediran, S. A., Kumar, I., Nagarajan, R., Sauvage, E., and Pratt, R. F. (2011) Kinetics of reactions of the Actinomadura R39 dd -peptidase with specific substrates Biochemistry 50, 376-387
Dzhekieva, L., Rocaboy, M., Kerff, F., Charlier, P., Sauvage, E., and Pratt, R. F. (2010) Crystal structure of a complex between the Actinomadura R39 dd -peptidase and a peptidoglycan-mimetic boronate inhibitor: Interpretation of a transition state analogue in terms of catalytic mechanism Biochemistry 49, 6411-6419
Sauvage, E., Herman, R., Petrella, S., Duez, C., Bouillenne, F., Frère, J.-M., and Charlier, P. (2005) Crystal structure of the Actinomadura R39 dd -peptidase reveals new domains in penicillin binding proteins J. Biol. Chem. 280, 31249-31256 (Pubitemid 41291862)
Nicholas, R. A., Krings, S., Tomberg, J., Nichola, G., and Davies, C. (2003) Crystal structures of wild-type penicillin-binding protein 5 from Escherichia coli J. Biol. Chem. 278, 52826-52833
Stevanova, M. E., Tomberg, J., Olesky, M., Höltje, 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 (Pubitemid 37532008)
Stefanova, M. E., Tomberg, J., Davies, C., Nicholas, R. A., and Gutheil, W. G. (2004) Overexpression and enzymatic characterization of Neisseria gonorrhoeae penicillin-binding protein 4 Eur. J. Biochem. 271, 23-32 (Pubitemid 38122162)
Duez, C., Van Hove, M., Gallet, X., Bouillene, F., Docquier, J.-D., Brous, A., and Frère, J.-M. (2001) Purification and characterization of PBP4a, a new low molecular-weight penicillin-binding protein from Bacillus subtilis J. Bacteriol. 183, 1595-1599 (Pubitemid 32172302)
Morlot, C., Pernot, L., Le Gouellec, A., Di Giulmi, A. M., Vernet, T., Dideberg, O., and Dessen, A. (2005) Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae J. Biol. Chem. 280, 15984-15991 (Pubitemid 40616722)
Anderson, J. W., Adediran, S. A., Charlier, P., Nguyen-Distèche, M., Frère, 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 (Pubitemid 36981106)
Josephine, H. R., Charlier, P., Davies, C., Nicholas, R. A., and Pratt, R. F. (2006) Reactivity of penicillin-binding proteins with peptidoglycan- mimetic β-lactams: What's wrong with these enzymes? Biochemistry 45, 15873-15883 (Pubitemid 46032508)
Garcia-Bustos, J. F., Chait, B. T., and Tomasz, A. (1987) Structure of the peptide network of pneumococcal peptidoglycan J. Biol. Chem. 262, 15400-15405
Severin, A. and Tomasz, A. (1996) Naturally occurring peptidoglycan variants of Streptococcus pneumoniae J. Bacteriol. 178, 168-174 (Pubitemid 26006080)
Tomasz, A. and Fischer, W. (2006) The cell wall of Streptococcus pneumoniae. In Gram-positive Pathogens (Fischetti, V. A., Novick, R. P., Ferretti, J. J., Portnoy, D. A., and Rood, J. I., Eds.) 2nd ed., pp 230-240, American Society for Microbiology Press, Washington, DC.
Sauvage, E., Powell, A. J., Heilemann, J., Josephine, H. R., Charlier, P., Davies, C., and Pratt, R. F. (2008) Crystal structures of complexes of bacterial dd -peptidases with peptidoglycan-mimetic ligands; the substrate specificity puzzle J. Mol. Biol. 381, 383-393
Nagarajan, R. and Pratt, R. F. (2004) Synthesis and evaluation of new substrate analogues of Streptomyces R61 dd -peptidase: Dissection of a specific ligand J. Org. Chem. 69, 7472-7478 (Pubitemid 39403332)
Duez, C., Zervosen, A., Teller, N., Melkonian, R., Banzubazé, Bouillenne, F., Luxen, A., and Frère, J.-M. (2009) Characterization of the proteins encoded by the Bacillus subtilis yoxA-dacC operon FEMS Microbiol. Lett. 300, 42-47
Sauvage, E., Duez, C., Herman, R., Kerff, F., Perrella, S., Anderson, J. W., Adediran, S. A., Pratt, R. F., Frère, J.-M., and Charlier, P. (2007) Crystal structure of the Bacillus subtilis penicillin-binding protein 4a and its complex with peptidoglycan-mimetic peptide J. Mol. Biol. 371, 528-539 (Pubitemid 47048282)
Macheboeuf, P., Lemaire, D., Dos Santos Martins, A., Dideberg, O., Jamin, M., and Dessen, A. (2008) Trapping of an acyl-enzyme intermediate in a penicillin binding protein (PBP)-catalyzed reaction J. Mol. Biol. 376, 405-413
Atrih, A., Bacher, G., Allmaier, G., Williamson, M. P., and Foster, S. J. (1999) Analysis of peptidoglycan structure from vegetative cells of B. subtilis 168 and role of PBP5 in peptidoglycan maturation J. Bacteriol. 181, 3956-3966 (Pubitemid 29295913)
Warth, A. D. and Strominger, J. L. (1971) Structure of the peptidoglycan from vegetative cell walls of Bacillus subtilis Biochemistry 10, 4349-4358
Pederson, L. B., Murray, T., Popham, D. L., and Setlow, P. (1998) Characterization of dacC, which encodes a new low-molecular-weight penicillin-binding protein in Bacillus subtilis J. Bacteriol. 180, 4967-4973 (Pubitemid 28429390)
Warth, A. D. and Strominger, J. L. (1969) Structure of the peptidoglycan of bacterial spores: Occurrences of the lactam of muramic acid Proc. Natl. Acad. Sci. U.S.A. 64, 528-535
Mattei, P.-J., Neves, D., and Dessen, A. (2010) Bridging cell wall biosynthesis and bacterial morphogenesis Curr. Opin. Struct. Biol. 20, 749-755
Typas, A., Banzhaf, M., van den Berg van Saparoea, B., Verheul, J., Biboy, J., Nichols, R. J., Zietek, M., Beilharz, K., Kannenberg, K., von Rechenberg, M., Breukink, E., den Blaauwen, T., Gross, C. A., and Vollmer, W. (2010) Regulation of peptidoglycan synthesis by outer-membrane proteins Cell 143, 1097-1109
Peddi, S., Nicholas, R. A., and Gutheil, W. G. (2009) Neisseria gonorrhoeae penicillin-binding protein 3 demonstrates a pronounced preference for Nε-acylated substrates Biochemistry 48, 5731-5737
Kishida, H., Unzai, S., Roper, D. I., Lloyd, A., Park, S.-Y., and Tame, J. R. H. (2006) Crystal structure of penicillin-binding protein 4 (Dac B) from Escherichia coli, both in the native form and covalently linked to various antibiotics Biochemistry 45, 783-792 (Pubitemid 43122243)
Kumar, I., Josephine, H. R., and Pratt, R. F. (2007) Reactions of peptidoglycan-mimetic β-lactams with penicillin-binding proteins in vivo and in membranes ACS Chem. Biol. 2, 620-624 (Pubitemid 350019779)
Nicola, G., Peddi, S., Stefanova, M., Nicholas, R. A., Gutheil, W. G., and Davies, C. (2005) Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: A role for Ser 110 in deacylation Biochemistry 44, 8207-8217 (Pubitemid 40799901)
Nelson, D. R., Ghosh, A. S., Paulson, A. L., and Young, K. D. (2002) Contribution of membrane-binding and enzymatic domains of penicillin-binding proteins to maintenance of uniform cellular morphology in Escherichia coli J. Bacteriol. 184, 3630-3639 (Pubitemid 34625672)
Potluri, L., Karczmarek, A., Verheul, J., Piette, A., Wilkin, J.-M., Werth, N., Banzhaf, N., Vollmer, W., Young, K. D., Nguyen-Distèche, M., and den Blaauwen, T. (2011) Septal and lateral wall localization of PBP5, the major dd -carboxypeptidase of Escherichia coli, requires substrate recognition and membrane attachment Mol. Microbiol. 77, 300-323
Pearson, W. R. (1996) Effective protein sequence comparison Methods Enzymol. 266, 227-258 (Pubitemid 26165871)
Romeis, T. and Holtje, J.-V. (1994) Penicillin-binding protein 7/8 of Escherichia coli is a dd -endopeptidase Eur. J. Biochem. 224, 597-604 (Pubitemid 24282845)
Amanuma, H. and Strominger, J. L. (1980) Purification and properties of penicillin-binding proteins 5 and 6 from Escherichia coli membranes J. Biol. Chem. 255, 11173-11180 (Pubitemid 11134233)
Van der Linden, M. P. G., de Haan, L., Hoger, M. A., and Keck, W. (1992) Possible role of Escherichia coli PBP6 in stabilization of stationary phase peptidoglycan J. Bacteriol. 174, 7572-7578
Chowdhury, C., Nayak, T. R., Young, K. D., and Ghosh, A. S. (2010) A weak dd -carboxypeptidase activity explains the inability of PBP6 to substitute for PBP5 in maintaining normal cell shape in Escherichia coli FEMS Microbiol. Lett. 303, 76-83
Chowdhury, C. and Ghosh, A. (2011) Differences in active site microarchitecture explain the dissimilar behaviors of PBP5 and PBP6 in Escherichia coli J. Mol. Graphics Modell. 29, 650-656
Chen, Y., Zhang, W., Shi, Q., Hesek, D., Lee, M., Mobashery, S., and Shoichet, B. K. (2009) Crystal structures of penicillin-binding protein 6 from Escherichia coli J. Am. Chem. Soc. 131, 14345-14354
Hesek, D., Suvorov, M., Morio, K., Lee, M., Brown, S., Vakulenko, S. B., and Mobashery, S. (2004) Synthetic peptidoglycan substrates for penicillin-binding protein 5 of Gram-negative bacteria J. Org. Chem. 69, 778-784 (Pubitemid 38168545)
Alaedini, A. and Day, R. A. (1999) Identification of two penicillin-binding multienzyme complexes in Haemophilus influenzae Biochem. Biophys. Res. Commun. 264, 191-195 (Pubitemid 29500486)
Lee, B. (1971) Conformation of penicillin as a transition-state analog of the substrate of peptidoglycan transpeptidase J. Mol. Biol. 61, 463-469
Pratt, R. F. (2008) Substrate specificity of bacterial dd -peptidases (penicillin-binding proteins) Cell. Mol. Life Sci. 65, 2138-2155
Terrak, M., Ghosh, T. K., van Heijenoort, J., Van Beeumen, J., Lampilis, M., Aszodi, J., Ayala, J. A., Ghuysen, J.-M., and Nguyen-Distèche, M. (1999) The catalytic glycosyl transferase and acyl transferase modules of the cell wall peptidoglycan-polymerizing penicillin-binding protein 1b of Escherichia coli Mol. Microbiol. 34, 350-364 (Pubitemid 29486252)
Lupoli, T. J., Tsukamoto, H., Doud, E. H., Wang, T.-S. A., Walker, S., and Kahne, D. (2011) Transpeptidase-mediated incorporation of d -amino acids into bacterial peptidoglycan J. Am. Chem. Soc. 133, 10748-10751
Macheboeuf, P., Di Giulmi, A. M., Job, V., Vernet, T., Dideberg, O., and Dessen, A. (2005) Active site restructuring regulates ligand recognition in class A penicillin-binding proteins Proc. Natl. Acad. Sci. U.S.A. 102, 577-582 (Pubitemid 40282707)
Lovering, A. L., DeCastro, L., Lim, D., and Strynadka, N. C. J. (2006) Structural analysis of an "open" form of PBP 1b from Streptococcus pneumoniae Protein Sci. 15, 1701-1709
Lim, D. and Strynadka, N. C. J. (2002) Structural basis for the β-lactam resistance of PBP 2a from methicillin-resistant Staphylococcus aureus Nat. Struct. Biol. 9, 870-876 (Pubitemid 35257789)
Fuda, C., Savarov, M., Vakulenko, S. B., and Mobashery, S. (2004) The basis for resistance to β-lactam antibiotics by penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus J. Biol. Chem. 279, 40802-40806 (Pubitemid 39287677)
Fuda, C., Hesek, D., Lee, M., Morio, K., Thomas, N., and Mobashery, S. (2005) Activation for catalysis of penicillin-binding protein 2a from methicillin-resistant Staphylococcus aureus by bacterial cell wall J. Am. Chem. Soc. 127, 2056-2057 (Pubitemid 40270504)
Chittock, R. S., Ward, S., Wilkinson, A.-S., Caspers, P., Mensch, B., Page, M. G. P., and Wharton, C. W. (1999) Hydrogen-bonding and protein perturbation in β-lactam acyl-enzymes of Streptococcus pneumoniae penicillin-binding protein PBP2x Biochem. J. 338, 153-159 (Pubitemid 29097298)
Zhao, G.-H., Duez, C., LePage, S., Forceille, C., Rhazi, N., Klein, D., Ghuysen, J.-M., and Frère, J.-M. (1997) Site-directed mutagenesis of the Actinomadura R39 dd -peptidase Biochem. J. 327, 377-381 (Pubitemid 27477811)
