3MXR: SHV-1 beta-lactamase complex with compound 1

Boronic acid transition state inhibitors (BATSIs) are potent class A and C beta-lactamase inactivators and are of particular interest due to their reversible nature mimicking the transition state. Here, we present structural and kinetic data describing the inhibition of the SHV-1 beta-lactamase, a clinically important enzyme found in Klebsiella pneumoniae, by BATSI compounds possessing the R1 side chains of ceftazidime and cefoperazone and designed variants of the latter, compounds 1 and 2. The ceftazidime and cefoperazone BATSI compounds inhibit the SHV-1 beta-lactamase with micromolar affinity that is considerably weaker than their inhibition of other beta-lactamases. The solved crystal structures of these two BATSIs in complex with SHV-1 reveal a possible reason for SHV-1's relative resistance to inhibition, as the BATSIs adopt a deacylation transition state conformation compared to the usual acylation transition state conformation when complexed to other beta-lactamases. Active-site comparison suggests that these conformational differences might be attributed to a subtle shift of residue A237 in SHV-1. The ceftazidime BATSI structure revealed that the carboxyl-dimethyl moiety is positioned in SHV-1's carboxyl binding pocket. In contrast, the cefoperazone BATSI has its R1 group pointing away from the active site such that its phenol moiety moves residue Y105 from the active site via end-on stacking interactions. To work toward improving the affinity of the cefoperazone BATSI, we synthesized two variants in which either one or two extra carbons were added to the phenol linker. Both variants yielded improved affinity against SHV-1, possibly as a consequence of releasing the strain of its interaction with the unusual Y105 conformation.
PDB ID: 3MXRDownload
MMDB ID: 86448
PDB Deposition Date: 2010/5/7
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.3  Å
Source Organism:
Similar Structures:
Biological Unit for 3MXR: monomeric; determined by author and by software (PISA)
Molecular Components in 3MXR
Label Count Molecule
Protein (1 molecule)
Beta-lactamase Shv-1
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

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