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See detailX-RAY STRUCTURES AND MECHANISMS OF METALLO-beta-LACTAMASES
Bebrone, Carine ULg; Garau, Gianpiero; Garcia-Saez, Isabel et al

in Frère, Jean-Marie (Ed.) Beta-Lactamases (Molecular Anatomy and Physiology of Proteins) (2012)

The metallo--lactamase superfamily comprises a remarkable set of enzymes that catalyse the hydrolysis of a wide range of substrates such as peptides, nucleic acids, antibiotics of the penicillin family ... [more ▼]

The metallo--lactamase superfamily comprises a remarkable set of enzymes that catalyse the hydrolysis of a wide range of substrates such as peptides, nucleic acids, antibiotics of the penicillin family and organophosphorus derivatives. In the past ten years, X-Ray structures of representative enzymes from different families have been determined, with the metallo--lactamases being the most represented. The salient common structural feature is the presence of a catalytic metal centre embedded within a  fold. The wealth of sequence and structural information on metallo--lactamases has allowed their classification into three subclasses. Structural information is now available for members of each subclass. Interestingly, these structures show the presence of either a mono or a di-nuclear metal centre in the active sites raising questions on the metal to protein stoichiometry under physiological conditions. In addition, the structures reveal a wide variability in the shape of the active site, which involves three variable loops lining the metal centre. For each enzyme a clear correlation is found between active site shape and substrate specificity. [less ▲]

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See detailMutational analysis of the zinc- and substrate-binding sites in the CphA metallo-beta-lactamase from Aeromonas hydrophila.
Bebrone, Carine ULg; Anne, Christine; Kerff, Frédéric ULg et al

in Biochemical Journal (2008), 414(1), 151-9

The subclass B2 CphA (Carbapenemase hydrolysing Aeromonas) beta-lactamase from Aeromonas hydrophila is a Zn(2+)-containing enzyme that specifically hydrolyses carbapenems. In an effort to evaluate ... [more ▼]

The subclass B2 CphA (Carbapenemase hydrolysing Aeromonas) beta-lactamase from Aeromonas hydrophila is a Zn(2+)-containing enzyme that specifically hydrolyses carbapenems. In an effort to evaluate residues potentially involved in metal binding and/or catalysis (His(118), Asp(120), His(196) and His(263)) and in substrate specificity (Val(67), Thr(157), Lys(224) and Lys(226)), site-directed mutants of CphA were generated and characterized. Our results confirm that the first zinc ion is in interaction with Asp(120) and His(263), and thus is located in the 'cysteine' zinc-binding site. His(118) and His(196) residues seem to be interacting with the second zinc ion, as their replacement by alanine residues has a negative effect on the affinity for this second metal ion. Val(67) plays a significant role in the binding of biapenem and benzylpenicillin. The properties of a mutant with a five residue (LFKHV) insertion just after Val(67) also reveals the importance of this region for substrate binding. This latter mutant has a higher affinity for the second zinc ion than wild-type CphA. The T157A mutant exhibits a significantly modified activity spectrum. Analysis of the K224Q and N116H/N220G/K224Q mutants suggests a significant role for Lys(224) in the binding of substrate. Lys(226) is not essential for the binding and hydrolysis of substrates. Thus the present paper helps to elucidate the position of the second zinc ion, which was controversial, and to identify residues important for substrate binding. [less ▲]

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See detailStructural basis for the broad-spectrum inhibition of metallo-beta-lactamases by thiols
Lienard, Benoit M R; Garau, Gianpiero; Horsfall, Louise et al

in Organic & Biomolecular Chemistry (2008), 6(13), 2282-2294

The development of broad-spectrum metallo-beta-lactamase (MBL) inhibitors is challenging due to structural diversity and differences in metal utilisation by these enzymes. Analysis of structural data ... [more ▼]

The development of broad-spectrum metallo-beta-lactamase (MBL) inhibitors is challenging due to structural diversity and differences in metal utilisation by these enzymes. Analysis of structural data, followed by non-denturing mass spectrometric analyses, identified thiols proposed to inhibit representative MBLs from all three sub-classes: B1, B2 and B3. Solution analyses led to the identification of broad spectrum inhibitors, including potent inhibitors of the CphA MBL (Aeromonas hydrophila). Structural studies revealed that, as observed for other B1 and B3 MBLs, inhibition of the L1 MBL thiols involves metal chelation. Evidence is reported that this is not the case for inhibition of the CphA enzyme by some thiols; the crystal structure of the CphA-Zn-inhibitor complex reveals a binding mode in which the thiol does not interact with the zinc. The structural data enabled the design and the production of further more potent inhibitors. Overall the results suggest that the development of reasonably broad-spectrum MBL inhibitors should be possible. [less ▲]

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See detailA metallo-beta-lactamase enzyme in action: Crystal structures of the monozinc carbapenemase CphA and its complex with biapenem
Garau, Gianpiero; Bebrone, Carine ULg; Anne, Christine et al

in Journal of Molecular Biology (2005), 345(4), 785-795

One strategy developed by bacteria to resist the action of beta-lactam antibiotics is the expression of metallo-beta-lactamases. CphA from Aeromonas hydrophila is a member of a clinically important ... [more ▼]

One strategy developed by bacteria to resist the action of beta-lactam antibiotics is the expression of metallo-beta-lactamases. CphA from Aeromonas hydrophila is a member of a clinically important subclass of metallo-beta-lactamases that have only one zinc ion in their active site and for which no structure is available. The crystal structures of wild-type CphA and its N220G mutant show the structural features of the active site of this enzyme, which is modeled specifically for carbapenem hydrolysis. The structure of CphA after reaction with a carbapenem substrate, biapenem, reveals that the enzyme traps a reaction intermediate in the active site. These three X-ray structures have allowed us to propose how the enzyme recognizes carbapenems and suggest a mechanistic pathway for hydrolysis of the beta-lactam. This will be relevant for the design of metallo-beta-lactamase inhibitors as well as of antibiotics that escape their hydrolytic activity. (C) 2004 Elsevier Ltd. All rights reserved. [less ▲]

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See detailIs it necessary to change the classification of ß-lactamases?
Frère, Jean-Marie ULg; Galleni, Moreno ULg; Bush, Karen et al

in Journal of Antimicrobial Chemotherapy (2005), 55(6), 1051-1053

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See detailThe 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold
Carfi, A.; Pares, S.; Duée, E. et al

in EMBO Journal (1995), 14(20), 4914-4921

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See detailPrimary and Predicted Secondary Structures of the Actinomadura R39 Extracellular DD-Peptidase, a Penicillin-Binding Protein (PBP) Related to the Escherichia coli PBP4
Granier, Benoît; Duez, Colette ULg; Englebert, Serge et al

in Biochemical Journal (1992), 282(Pt 3), 781-788

As derived from gene cloning and sequencing, the 489-amino-acid DD-peptidase/penicillin-binding protein (PBP) produced by Actinomadura R39 has a primary structure very similar to that of the Escherichia ... [more ▼]

As derived from gene cloning and sequencing, the 489-amino-acid DD-peptidase/penicillin-binding protein (PBP) produced by Actinomadura R39 has a primary structure very similar to that of the Escherichia coli PBP4 [Mottl, Terpstra & Keck (1991) FEMS Microbiol. Lett. 78, 213-220]. Hydrophobic-cluster analysis of the two proteins shows that, providing that a large 174-amino-acid stretch is excluded from the analysis, the bulk of the two polypeptide chains possesses homologues of the active-site motifs and secondary structures found in the class A β-lactamase of Streptomyces albus G of known three-dimensional structure. The 74-amino-acid insert occurs at equivalent places in the two PBPs, between helices α2 and α3, away from the active site. Such an insert is unique among the penicilloyl serine transferases. It is proposed that the Actinomadura R39 PBP and E. coli PBP4 form a special class, class C, of low-Mr PBPs/DD-peptidases. A vector has been constructed and introduced by electrotransformation in the original Actinomadura R39 strain, allowing high-level expression and secretion of the DD-peptidase/PBP (250 mg . 1-1). The gene encoding the desired protein is processed differently in Actinomadura R39 and Streptomyces lividans. Incorrect processing in Streptomyces lividans leads to a secreted protein which is inert in terms of DD-peptidase activity and penicillin-binding capacity. [less ▲]

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See detailMechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G
Lamotte-Brasseur, Josette; Dive, Georges ULg; Dideberg, Otto et al

in Biochemical Journal (1991), 279(Pt 1), 213-221

Optimization by energy minimization of stable complexes occurring along the pathway of hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase has highlighted a ... [more ▼]

Optimization by energy minimization of stable complexes occurring along the pathway of hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase has highlighted a proton shuttle that may explain the catalytic mechanism of the beta-lactamases of class A. Five residues, S70, S130, N132, T235 and A237, are involved in ligand binding. The gamma-OH group of T235 and, in the case of benzylpenicillin, the gamma-OH group of S130 interact with the carboxylate group, on one side of the ligand molecule. The side-chain NH2 group of N132 and the carbonyl backbone of A237 interact with the exocyclic CONH amide bond, on the other side of the ligand. The backbone NH groups of S70 and A237 polarize the carbonyl group of the scissile beta-lactam amide bond. Four residues, S70, K73, S130 and E166, and two water molecules, W1 and W2, perform hydrolysis of the bound beta-lactam compound. E166, via W1, abstracts the proton from the gamma-OH group of S70. While losing its proton, the O-gamma atom of S70 attacks the carbonyl carbon atom of the beta-lactam ring and, concomitantly, the proton is delivered back to the adjacent nitrogen atom via W2, K73 and S130, thus achieving formation of the acyl-enzyme. Subsequently, E166 abstracts a proton from W1. While losing its proton, W1 attacks the carbonyl carbon atom of the S70 ester-linked acyl-enzyme and, concomitantly, re-entry of a water molecule W'1 replacing W1 allows E166 to deliver the proton back to the same carbonyl carbon atom, thus achieving hydrolysis of the beta-lactam compound and enzyme recovery. The model well explains the differences found in the kcat. values for hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase. It also explains the effects caused by site-directed mutagenesis of the Bacillus cereus beta-lactamase I [Gibson, Christensen [less ▲]

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See detailAmino Acid Sequence of the Penicillin-Binding Protein/DD-Peptidase of Streptomyces K15. Predicted Secondary Structures of the Low Mr Penicillin-Binding Proteins of Class A
Palomeque-Messia, Pilar; Englebert, Serge; Leyh-Bouille, Melina et al

in Biochemical Journal (1991), 279(Pt 1), 223-230

The low-Mr penicillin-binding protein (PBP)/DD-transpeptidase of Streptomyces K15 is synthesized in the form of a 291-amino acid-residue precursor possessing a cleavable 29-amino acid-residue signal ... [more ▼]

The low-Mr penicillin-binding protein (PBP)/DD-transpeptidase of Streptomyces K15 is synthesized in the form of a 291-amino acid-residue precursor possessing a cleavable 29-amino acid-residue signal peptide. Sequence-similarity searches and hydrophobic-cluster analysis show that the Streptomyces K15 enzyme, the Escherichia coli PBPs/DD-carboxy-peptidases 5 and 6, the Bacillus subtilis PBP/DD-carboxypeptidase 5 and the spoIIA product (a putative PBP involved in the sporulation of B. subtilis) are structurally related and form a distinct class A of low-Mr PBPs/DD-peptidases. The distribution of the hydrophobic clusters along the amino acid sequences also shows that the Streptomyces K15 PBP, and by extension the other PBPs of class A, have similarity in the polypeptide folding, with the beta-lactamases of class A, with as reference the Streptomyces albus G and Staphylococcus aureus beta-lactamases of known three-dimensional structure. This comparison allows one to predict most of the secondary structures in the PBPs and the amino acid motifs that define the enzyme active sites. [less ▲]

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See detailRevision of the Structure of Strychnochromine
Quetin-Leclercq, Joëlle; Angenot, Luc ULg; Dupont, Léon et al

in Tetrahedron Letters (1991), 32(34), 4295-4298

The structure of strychnochromine, an unusual alkaloid isolated from a new batch of the root bark of Strychnos gossweileri has been revised . To confirm the indoline structure ( proposed in 1988) and to ... [more ▼]

The structure of strychnochromine, an unusual alkaloid isolated from a new batch of the root bark of Strychnos gossweileri has been revised . To confirm the indoline structure ( proposed in 1988) and to establish the stereochemistry of the compound extensive 2D-NMR experiments were carried out. The COSY experiments mostly confirmed the previous observations but the COLOC maps did not fit the first proposed structure!The problem was solved by single-crystal X-ray analysis of the p-bromobenzoyl ester of strychnochromine. The new structure, with its tetrahydroquinoline ring, is very unusual in Strychnos species but the formation of quinolines from indole alkaloids has already mentioned in some other plants ( Cinchona, Alstonia, Hunteria..). [less ▲]

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See detailThe Active-Site-Serine Penicillin-Recognizing Enzymes as Members of the Streptomyces R61 Dd-Peptidase Family
Joris, Bernard ULg; Ghuysen, Jean-Marie ULg; Dive, Georges ULg et al

in Biochemical Journal (1988), 250(2), 313-324

Homology searches and amino acid alignments, using the Streptomyces R61 DD-peptidase/penicillin-binding protein as reference, have been applied to the beta-lactamases of classes A and C, the Oxa-2 beta ... [more ▼]

Homology searches and amino acid alignments, using the Streptomyces R61 DD-peptidase/penicillin-binding protein as reference, have been applied to the beta-lactamases of classes A and C, the Oxa-2 beta-lactamase (considered as the first known member of an additional class D), the low-Mr DD-peptidases/penicillin-binding proteins (protein no. 5 of Escherichia coli and Bacillus subtilis) and penicillin-binding domains of the high-Mr penicillin-binding proteins (PBP1A, PBP1B, PBP2 and PBP3 of E. coli). Though the evolutionary distance may vary considerably, all these penicillin-interactive proteins and domains appear to be members of a single superfamily of active-site-serine enzymes distinct from the classical trypsin or subtilisin families. The amino acid alignments reveal several conserved boxes that consist of strict identities or homologous amino acids. The significance of these boxes is highlighted by the known results of X-ray crystallography, chemical derivatization and site-directed-mutagenesis experiments. [less ▲]

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See detailProperties and crystallization of a genetically engineered, water-soluble derivative of penicillin-binding protein 5 of Escherichia coli K12
Ferreira, Luis C; Schwarz, Uli; Keck, Wolfgang et al

in European Journal of Biochemistry (1988), 171(1-2), 11-16

Derivatives of the Escherichia coli penicillin-binding protein 5 (PBP5) with truncated carboxyl terminals were obtained by altering the carboxyl-coding end of the dacA gene. After cloning the modified ... [more ▼]

Derivatives of the Escherichia coli penicillin-binding protein 5 (PBP5) with truncated carboxyl terminals were obtained by altering the carboxyl-coding end of the dacA gene. After cloning the modified dacA gene into a runaway-replication-control plasmid, one clone that overproduced and excreted the desired protein into the periplasm was used as a source for the isolation of a water-soluble PBP5 (i.e. PBP5S). In PBP5S the carboxyl-terminal 21-amino-acid region of the wild-type protein was replaced by a short 9-amino-acid segment. Milligram amounts of PBP5S were purified by penicillin affinity chromatography in the absence of detergents or of chaotropic agents. PBP5S was stable and possessed DD-carboxypeptidase activity without added Triton X-100. Upon reaction with [14C]benzylpenicillin it was converted into a rather short-lived acyl-enzyme complex, as observed with PBP5. Both PBP5 and PBP5S were crystallized. In contrast to PBP5, PBP5S yielded enzymatically active, well-formed prismatic crystals suitable for X-ray analysis. [less ▲]

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See detailPenicillin-recognizing enzymes
Frère, Jean-Marie ULg; Joris, Bernard ULg; Dideberg, Otto et al

in Biochemical Society Transactions (1988), 16(6), 934-938

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See detailThe crystal structure of the β-lactamase of Streptomyces albus G at 0.3 nm resolution
Dideberg, Otto; Charlier, Paulette ULg; Wery, Jean-Paul et al

in Biochemical Journal (1987), 245(3), 911-913

The crystal structure of the beta-lactamase of Streptomyces albus G has been solved at 0.3 nm resolution by X-ray-diffraction methods. The enzyme is a typical two-domain protein. One domain consists of ... [more ▼]

The crystal structure of the beta-lactamase of Streptomyces albus G has been solved at 0.3 nm resolution by X-ray-diffraction methods. The enzyme is a typical two-domain protein. One domain consists of five alpha-helices, and the other is five-stranded beta-sheet with alpha-helices on both sides of the sheet. The active-site serine residue (Ser-48) is within a cleft located between the two domains. [less ▲]

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See detailOn the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target
Kelly, Judith A.; Dideberg, Otto; Charlier, Paulette ULg et al

in Science (1986), 231

Structural data are now available for comparing a penicillin target enzyme, the D-alanyl-D-alanine-peptidase from Streptomyces R61, with a penicillin-hydrolyzing enzyme, the beta-lactamase from Bacillus ... [more ▼]

Structural data are now available for comparing a penicillin target enzyme, the D-alanyl-D-alanine-peptidase from Streptomyces R61, with a penicillin-hydrolyzing enzyme, the beta-lactamase from Bacillus licheniformis 749/C. Although the two enzymes have distinct catalytic properties and lack relatedness in their overall amino acid sequences except near the active-site serine, the significant similarity found by x-ray crystallography in the spatial arrangement of the elements of secondary structure provides strong support for earlier hypotheses that beta-lactamases arose from penicillin-sensitive D-alanyl-D-alanine-peptidases involved in bacterial wall peptidoglycan metabolism. [less ▲]

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See detailActive-site-directed inactivators of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G.
Charlier, Paulette ULg; Dideberg, Otto; Jamoulle, Jean-Claude et al

in Biochemical Journal (1984), 219(3), 763-772

Several types of active-site-directed inactivators (inhibitors) of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase were tested. (i) Among the heavy-atom-containing compounds examined ... [more ▼]

Several types of active-site-directed inactivators (inhibitors) of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase were tested. (i) Among the heavy-atom-containing compounds examined, K2Pt(C2O4)2 inactivates the enzyme with a second-order rate constant of about 6 X 10(-2)M-1 X S-1 and has only one binding site located close to the Zn2+ cofactor within the enzyme active site. (ii) Several compounds possessing both a C-terminal carboxylate function and, at the other end of the molecule, a thiol, hydroxamate or carboxylate function were also examined. 3-Mercaptopropionate (racemic) and 3-mercaptoisobutyrate (L-isomer) inhibit the enzyme competitively with a Ki value of 5 X 10 X 10(-9)M. (iii) Classical beta-lactam compounds have a very weak inhibitory potency. Depending on the structure of the compounds, enzyme inhibition may be competitive (and binding occurs to the active site) or non-competitive (and binding causes disruption of the protein crystal lattice). (iv) 6-beta-Iodopenicillanate inactivates the enzyme in a complex way. At high beta-lactam concentrations, the pseudo-first-order rate constant of enzyme inactivation has a limit value of 7 X 10(-4)S-1 X 6-beta-Iodopenicillanate binds to the active site just in front of the Zn2+ cofactor and superimposes histidine-190, suggesting that permanent enzyme inactivation is by reaction with this latter residue. [less ▲]

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See detailStudy of the Zn-containing DD-carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution.
Labischinski, Harald; Giesbrecht, Peter; Fischer, E. et al

in European Journal of Biochemistry (1984), 138(1), 83-87

Study of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution yielded the following molecular parameters: radius of gyration ... [more ▼]

Study of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G by small-angle X-ray scattering in solution yielded the following molecular parameters: radius of gyration R = 1.82 +/- 0.05 nm; largest diameter D = 5.9 +/- 0.2 nm; relative molecular mass Mr = 17000 +/- 2000; volume V approximately equal to 35 +/- 2 nm3; degree of hydration: 0.25 +/- 0.02 g water/g protein. By reference to theoretical scattering curves of rigid triaxial homogeneous bodies, a model which fits all experimental data is an elliptical cylinder. Such a model is compatible with that observed in the crystal structure. At those high concentrations necessary to form inactive enzyme-ligand associations the non-competitive beta-lactam inhibitors, cephalothin and cephalosporin C, drastically altered the scattering behaviour of the protein. [less ▲]

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See detailBacterial wall peptidoglycan, DD-peptidases and beta-lactam antibiotics
Ghuysen, Jean-Marie ULg; Frère, Jean-Marie ULg; Leyh-Bouille, Mélina et al

in Scandinavian Journal of Infectious Diseases (1984), 42

Wall peptidoglycan expansion in bacteria rests upon a cytoplasmic D-Ala: D-Ala ligase (ADP) which catalyses synthesis of a D-Ala-D-Ala dipeptide (with accompanying hydrolysis of one molecule of ATP) and a ... [more ▼]

Wall peptidoglycan expansion in bacteria rests upon a cytoplasmic D-Ala: D-Ala ligase (ADP) which catalyses synthesis of a D-Ala-D-Ala dipeptide (with accompanying hydrolysis of one molecule of ATP) and a set of DD-peptidases which utilize this D-Ala-D-Ala dipeptide--once it has been translocated at the outer face of the plasma membrane as the C-terminal portion of a disaccharide peptide unit--as carbonyl donor for transpeptidation and carboxypeptidation reactions (without additional energy expenditure). Four DD-peptidases have been selected which differ from each other with respect to the effects that amino compounds exert on the fate and rate of consumption of a D-Ala-D-Ala terminated amide carbonyl donor analogue. They serve as models to understand the different mechanisms by which the DD-peptidases perform catalysis and show widely varying responses to the action of beta-lactams, from extreme sensitivity to very high resistance. [less ▲]

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See detailInstrinct Resistance to beta-lactam antibiotics at the level of the enzyme sites. Many challenges, some achievements
Ghuysen, Jean-Marie ULg; Charlier, P.; Coyette, Jean et al

in Wiedemann, B.; Guysen, Jean-Marie; Spitzy, K. H. (Eds.) et al Symposium Mechanisms of resistance to beta-lactam antibiotics : Proceedings (1983)

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See detailThe active sites of the D-alanyl-D-alanine-cleaving peptidases
Charlier, Paulette ULg; Dideberg, Otto; Dive, Georges ULg et al

in Hakenbeck, Regine; Höltje, Joachim-Volker; Labischinski, Harald (Eds.) The Target Penicillin : the Murein Sacculus of Bacterial Cell Walls Architecture and Growth : Proceedings (1983)

The active site structures of D-alanyl-D-alanine-cleaving peptidases G, R61, R39, and K15 from Streptomyces and Actinomadura are discussed in relation to their substrate specificities and kinetic ... [more ▼]

The active site structures of D-alanyl-D-alanine-cleaving peptidases G, R61, R39, and K15 from Streptomyces and Actinomadura are discussed in relation to their substrate specificities and kinetic mechanisms. [less ▲]

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