3PAG: Crystal Structure Of The V130d Mutant Of Oxa-24/40 In Complex With Doripenem

Citation:
Abstract
The emergence of class D beta-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D beta-lactamases with carbapenemase activity are resistant to beta-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6alpha hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.
PDB ID: 3PAGDownload
MMDB ID: 88094
PDB Deposition Date: 2010/10/19
Updated in MMDB: 2015/11
Experimental Method:
x-ray diffraction
Resolution: 2.25  Å
Source Organism:
Similar Structures:
Biological Unit for 3PAG: monomeric; determined by author and by software (PISA)
Molecular Components in 3PAG
Label Count Molecule
Protein (1 molecule)
1
Beta-lactamase
Molecule annotation
Chemicals (5 molecules)
1
1
2
4
* Click molecule labels to explore molecular sequence information.

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