5hh5

From Proteopedia

Crystal structure of B3 metallo-beta-lactamase L1 complexed with a phosphonate-based inhibitor

PDB ID 5hh5

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Structural highlights

5hh5 is a 1 chain structure with sequence from Stenotrophomonas maltophilia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BLA1_STEMA Has a high activity against imipenem.

Publication Abstract from PubMed

There are currently no clinically available inhibitors of metallo-beta-lactamases (MBLs), enzymes that hydrolyze beta-lactam antibiotics and confer resistance to Gram-negative bacteria. Here we present 6-phosphonomethylpyridine-2-carboxylates (PMPCs) as potent inhibitors of subclass B1 (IMP-1, VIM-2, and NDM-1) and B3 (L1) MBLs. Inhibition followed a competitive, slow-binding model without an isomerization step (IC50 values of 0.3-7.2 muM; Ki values of 0.03-1.5 muM). Minimum inhibitory concentration assays demonstrated potentiation of beta-lactam (Meropenem) activity against MBL-producing bacteria, including clinical isolates, at concentrations at which eukaryotic cells remain viable. Crystal structures revealed unprecedented modes of binding of inhibitor to B1 (IMP-1) and B3 (L1) MBLs. In IMP-1, binding does not replace the nucleophilic hydroxide, and the PMPC carboxylate and pyridine nitrogen interact closely (2.3 and 2.7 A, respectively) with the Zn2 ion of the binuclear metal site. The phosphonate group makes limited interactions but is 2.6 A from the nucleophilic hydroxide. Furthermore, the presence of a water molecule interacting with the PMPC phosphonate and pyridine N-C2 pi-bond, as well as the nucleophilic hydroxide, suggests that the PMPC binds to the MBL active site as its hydrate. Binding is markedly different in L1, with the phosphonate displacing both Zn2, forming a monozinc enzyme, and the nucleophilic hydroxide, while also making multiple interactions with the protein main chain and Zn1. The carboxylate and pyridine nitrogen interact with Ser221 and -223, respectively (3 A distance). The potency, low toxicity, cellular activity, and amenability to further modification of PMPCs indicate these and similar phosphonate compounds can be further considered for future MBL inhibitor development.

Structural and Kinetic Studies of the Potent Inhibition of Metallo-beta-lactamases by 6-Phosphonomethylpyridine-2-carboxylates.,Hinchliffe P, Tanner CA, Krismanich AP, Labbe G, Goodfellow VJ, Marrone L, Desoky AY, Calvopina K, Whittle EE, Zeng F, Avison MB, Bols NC, Siemann S, Spencer J, Dmitrienko GI Biochemistry. 2018 Mar 27;57(12):1880-1892. doi: 10.1021/acs.biochem.7b01299., Epub 2018 Mar 9. PMID:29485857^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hinchliffe P, Tanner CA, Krismanich AP, Labbe G, Goodfellow VJ, Marrone L, Desoky AY, Calvopina K, Whittle EE, Zeng F, Avison MB, Bols NC, Siemann S, Spencer J, Dmitrienko GI. Structural and Kinetic Studies of the Potent Inhibition of Metallo-beta-lactamases by 6-Phosphonomethylpyridine-2-carboxylates. Biochemistry. 2018 Mar 27;57(12):1880-1892. doi: 10.1021/acs.biochem.7b01299., Epub 2018 Mar 9. PMID:29485857 doi:http://dx.doi.org/10.1021/acs.biochem.7b01299