3A9L

Structure of Bacteriophage poly-gamma-glutamate hydrolase

Summary for 3A9L

• Entry DOI: 10.2210/pdb3a9l/pdb
• Descriptor: Poly-gamma-glutamate hydrolase, ZINC ION, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: zinc ion binding, open alpha/beta mixed core structure, hydrolase
• Biological source: Bacillus phage phiNIT1
• Total number of polymer chains: 2
• Total formula weight: 48388.06

Authors

Fujimoto, Z.,Kimura, K. (deposition date: 2009-10-30, release date: 2010-11-10, Last modification date: 2024-03-13)

Primary citation

Fujimoto, Z.,Kimura, K.
Crystal structure of bacteriophage PhiNIT1 zinc peptidase PghP that hydrolyzes gamma-glutamyl linkage of bacterial poly-gamma-glutamate
Proteins, 80:722-732, 2012

PubMed Abstract: Poly-γ-glutamate hydrolase P (PghP) of Bacillus subtilis bacteriophage ΦNIT1 hydrolyzes the γ-glutamyl peptide linkage of extracellular poly-γ-glutamate produced by bacilli, which facilitates infection and propagation of phage progenies. Crystal structure of PghP was determined at a resolution of 1.9 Å. Structure of PghP was elucidated as a globular protein with an open α/β mixed core structure and a seven-stranded parallel/anti-parallel β-sheet. The β-sheet contained a core four-stranded parallel β-sheet. A zinc-binding motif, His-Glu-His, was identified at the C-terminal end of the β-sheet. Structure analysis demonstrated that PghP, which had not been previously classified into any peptidase/protease family due to lack of amino acid sequence similarity with known enzymes, had a catalytic center containing a zinc ion and an overall topology resembling mammalian carboxypeptidase A and related enzymes. Structural comparisons indicated important amino acid residues of PghP for catalysis and recognition of the γ-peptide bond of poly-γ-glutamate, which was confirmed by site-directed mutagenesis of PghP.

PubMed: 22105902
DOI: 10.1002/prot.23229

Experimental method

X-RAY DIFFRACTION (1.9 Å)