PDBsum entry: 1h8y

Hydrolase

PDB id: 1h8y

Contents

Protein chains

247 a.a. *

Ligands

MER ×2

SO4 ×4

Waters ×324

* Residue conservation analysis

PDB id:

1h8y

Name:

Hydrolase

Title:

Crystal structure of the class d beta-lactamase oxa-13 in complex with meropenem

Structure:

Beta-lactamase. Chain: a, b. Synonym: beta-lactamase oxa-13. Engineered: yes. Other_details: there is an ester link between ser a 67 og and mer a 300 c7 and between ser b 67 og and mer b 300 c7

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pae391. Gene: bla oxa-13. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.204 R-free: 0.257

Authors:

L.Pernot,F.Frenois,T.Rybkine,G.L'Hermite,S.Petrella, J.Delettre,V.Jarlier,E.Collatz,W.Sougakoff

Key ref:

L.Pernot et al. (2001). Crystal structures of the class D beta-lactamase OXA-13 in the native form and in complex with meropenem. J Mol Biol, 310, 859-874. PubMed id: 11453693 DOI: 10.1006/jmbi.2001.4805

Date:

17-Feb-01 Release date: 12-Jul-01

Protein chains

Q51400  (Q51400_PSEAE) -  Beta-lactamase

Seq: 266 a.a.

Struc: 247 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: peptidoglycan-based cell wall biogenesis (2 terms)
• Biochemical function: penicillin binding (2 terms)

DOI no: 10.1006/jmbi.2001.4805

J Mol Biol 310:859-874 (2001)

PubMed id: 11453693

Crystal structures of the class D beta-lactamase OXA-13 in the native form and in complex with meropenem.

L.Pernot, F.Frénois, T.Rybkine, G.L'Hermite, S.Petrella, J.Delettré, V.Jarlier, E.Collatz, W.Sougakoff.

ABSTRACT

The therapeutic problems posed by class D beta-lactamases, a family of serine enzymes that hydrolyse beta-lactam antibiotics following an acylation-deacylation mechanism, are increased by the very low level of sensitivity of these enzymes to beta-lactamase inhibitors. To gain structural and mechanistic insights to aid the design of new inhibitors, we have determined the crystal structure of OXA-13 from Pseudomonas aeruginosa in the apo form and in complex with the carbapenem meropenem. The native form consisted of a dimer displaying an overall organisation similar to that found in the closely related enzyme OXA-10. In the acyl-enzyme complex, the positioning of the antibiotic appeared to be ensured mainly by (i) the covalent acyl bond and (ii) a strong salt-bridge involving the carboxylate moiety of the drug. Comparison of the structures of OXA-13 in the apo form and in complex with meropenem revealed an unsuspected flexibility in the region of the essential serine 115 residue, with possible consequences for the catalytic properties of the enzyme. In the apo form, the Ser115 side-chain is oriented outside the active site, whereas the general base Lys70 adopts a conformation that seems to be incompatible with the activation of the catalytic water molecule required for the deacylation step. In the OXA-13:meropenem complex, a 3.5 A movement of the backbone of the 114-116 loop towards the side-chain of Lys70 was observed, which seems to be driven by a displacement of the neighbouring 91-104 loop and which results in the repositioning of the side-chain hydroxyl group of Ser115 toward the catalytic centre. Concomitantly, the side-chain of Lys70 is forced to curve in the direction of the deacylating water molecule, which is then strongly bound and activated by this residue. However, a distance of ca 5 A separates the catalytic water molecule from the acyl carbonyl group of meropenem, a structural feature that accounts for the inhibition of OXA-13 by this drug. Finally, the low level of penicillinase activity revealed by the kinetic analysis of OXA-13 could be related to the specific presence in position 73 of a serine residue located close to the general base Lys70, which results in a decrease of the number of hydrogen-bonding interactions stabilising the catalytic water molecule.

Selected figure(s)

Figure 1.
Figure 1. Superposition of the protein folds of OXA-13 in the native form (green ribbon) and in complex with meropenem (red ribbon). Meropenem (stick representation) is in pink. Water molecules are depicted using red spheres. Hydrogen bonds are shown as green broken lines.

Figure 2.
Figure 2. (a) Superimposition of the active site of OXA-13 (CPK colours) to OXA-10 (in blue, PDB accession code 1FOF). The protein backbones are shown, with the residues of interest in stick form. Hydrogen bonds are depicted by green broken lines. In the OXA-13 model, oxygen atoms are coloured red, carbon atoms gray and nitrogen atoms blue. The water molecules (HOH) are indicated by red and blue spheres in OXA-13 and OXA-10, respectively. The sulfate ion found in the active site of OXA-13 is shown in yellow and red. (b) Detailed view of the superimposition of OXA-13 (CPK colours) and OXA-10 (PDB entry code 1FOF ; in blue) in the 70-73 region.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 859-874) copyright 2001.

Figures were selected by an automated process.