5D2R

Inhibitor Bound Cell Shape Determinant Protein Csd4 from Helicobacter pylori

5D2R の概要

• エントリーDOI: 10.2210/pdb5d2r/pdb
• 分子名称: Conserved hypothetical secreted protein, ZINC ION, IODIDE ION, ... (5 entities in total)
• 機能のキーワード: mixed alpha beta sandwich, carboxypeptidase, m14, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Helicobacter pylori
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 53182.34

構造登録者

Chan, A.C.,Murphy, M.E. (登録日: 2015-08-06, 公開日: 2016-01-20, 最終更新日: 2023-09-27)

主引用文献

Liu, Y.,Frirdich, E.,Taylor, J.A.,Chan, A.C.,Blair, K.M.,Vermeulen, J.,Ha, R.,Murphy, M.E.,Salama, N.R.,Gaynor, E.C.,Tanner, M.E.
A Bacterial Cell Shape-Determining Inhibitor.
Acs Chem.Biol., 11:981-991, 2016

PubMed Abstract: Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials against these human pathogens.

PubMed: 26735022
DOI: 10.1021/acschembio.5b01039

実験手法

X-RAY DIFFRACTION (1.9 Å)