3A9L

Structure of Bacteriophage poly-gamma-glutamate hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of bacteriophage PhiNIT1 zinc peptidase PghP that hydrolyzes gamma-glutamyl linkage of bacterial poly-gamma-glutamate

Fujimoto, Z.Kimura, K.

(2012) Proteins 80: 722-732

  • DOI: 10.1002/prot.23229

  • 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 stru ...

    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.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of poly-gamma-glutamate hydrolase from bacteriophage PhiNIT1
      Fujimoto, Z.,Shiga, I.,Itoh, Y.,Kimura, K.
      (2009) Acta Crystallogr.,Sect.F 65: 913
    • Characterization of poly-gamma-glutamate hydrolase encoded by a bacteriophage genome: possible role in phage infection of Bacillus subtilis encapsulated with poly-gamma-glutamate
      Kimura, K.,Itoh, Y.
      (2003) Appl.Environ.Microbiol. 69: 2491


    Organizational Affiliation

    Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. zui@affrc.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly-gamma-glutamate hydrolase
A, B
216Bacillus phage phiNIT1Mutation(s): 0 
Gene Names: pghP
Find proteins for Q852V1 (Bacillus phage phiNIT1)
Go to UniProtKB:  Q852V1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.281 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 86.809α = 90.00
b = 86.809β = 90.00
c = 85.116γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
UGUI@PFdata collection
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-29
    Type: Database references