21DC

Crystal structure of poly-gamma-glutamate hydrolase from Bacillus phage PM1

21DC の概要

• エントリーDOI: 10.2210/pdb21dc/pdb
• 分子名称: Poly-gamma-glutamate hydrolase, DI(HYDROXYETHYL)ETHER, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: poly-gamma-glutamate hydrolase, bacillus phage, metallo peptidase, zinc, hydrolase
• 由来する生物種: Bacillus phage PM1
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27536.35

構造登録者

Abe, K.,Fukui, K.,Ogura, Y. (登録日: 2025-12-09, 公開日: 2026-04-08)

主引用文献

Abe, K.,Fukui, K.,Ogura, Y.
Crystal structure of PM1Pgh, a poly-gamma-glutamate hydrolase from Bacillus phage PM1.
Acta Crystallogr.,Sect.F, 82:136-142, 2026

PubMed Abstract: Poly-γ-glutamate (γ-PGA) is the key biopolymer responsible for the characteristic viscosity of natto, a traditional Japanese food produced by Bacillus subtilis var. natto. Phage infection frequently leads to γ-PGA degradation and loss of viscosity, a longstanding problem in natto production. While the γ-PGA hydrolase PghP from phage ΦNIT1 has been well characterized, the homologous enzyme encoded by B. subtilis var. natto phage PM1 has remained unstudied and is currently annotated only as ORF34; this protein is referred to here as PM1Pgh. Two catalytic models have been proposed for γ-PGA-degrading metallopeptidases: a direct anhydride mechanism involving the catalytic glutamate and a zinc-dependent, water-mediated mechanism. However, no definitive structural evidence has been obtained to distinguish between these mechanisms. Here, recombinant PM1Pgh was shown to possess γ-PGA hydrolase activity in vitro, and its crystal structures were determined in both zinc-free and zinc-bound states. The zinc-bound structure revealed a Zn ion specifically coordinated within the catalytic pocket together with a well ordered water molecule positioned for nucleophilic attack, supporting a zinc-dependent, water-mediated mechanism for γ-PGA hydrolysis, consistent with the canonical mechanism of metallopeptidases.

PubMed: 41879646
DOI: 10.1107/S2053230X26002189

実験手法

X-RAY DIFFRACTION (1.2 Å)