3MKE

SHV-1 beta-lactamase complex with LP06

Summary for 3MKE

• Entry DOI: 10.2210/pdb3mke/pdb
• Related: 3MKF
• Descriptor: Beta-lactamase SHV-1, CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE, PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE, ... (5 entities in total)
• Functional Keywords: beta-lactamase, boronic acid transition state inhibitor, drug design, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 30666.61

Authors

van den Akker, F.,Ke, W. (deposition date: 2010-04-14, release date: 2010-11-24, Last modification date: 2023-09-06)

Primary citation

Ke, W.,Sampson, J.M.,Ori, C.,Prati, F.,Drawz, S.M.,Bethel, C.R.,Bonomo, R.A.,van den Akker, F.
Novel Insights into the Mode of Inhibition of Class A SHV-1 {beta}-Lactamases Revealed by Boronic Acid Transition State Inhibitors.
Antimicrob.Agents Chemother., 55:174-183, 2011

PubMed Abstract: Boronic acid transition state inhibitors (BATSIs) are potent class A and C β-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 β-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 β-lactamase with micromolar affinity that is considerably weaker than their inhibition of other β-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 β-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.

PubMed: 21041505
DOI: 10.1128/AAC.00930-10

Experimental method

X-RAY DIFFRACTION (1.75 Å)