3A75

Crystal structure of glutamate complex of halotolerant γ-glutamyltranspeptidase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the halotolerant gamma-glutamyltranspeptidase from Bacillus subtilis in complex with glutamate reveals a unique architecture of the solvent-exposed catalytic pocket

Wada, K.Irie, M.Suzuki, H.Fukuyama, K.

(2010) Febs J. 277: 1000-1009

  • DOI: 10.1111/j.1742-4658.2009.07543.x

  • PubMed Abstract: 
  • gamma-Glutamyltranspeptidase (GGT; EC 2.3.2.2), an enzyme found in organisms from bacteria to mammals and plants, plays a central role in glutathione metabolism. Structural studies of GGTs from Escherichia coli and Helicobacter pylori have revealed d ...

    gamma-Glutamyltranspeptidase (GGT; EC 2.3.2.2), an enzyme found in organisms from bacteria to mammals and plants, plays a central role in glutathione metabolism. Structural studies of GGTs from Escherichia coli and Helicobacter pylori have revealed detailed molecular mechanisms of catalysis and maturation. In these two GGTs, highly conserved residues form the catalytic pockets, conferring the ability of the loop segment to shield the bound gamma-glutamyl moiety from the solvent. Here, we have examined the Bacillus subtilis GGT, which apparently lacks the amino acids corresponding to the lid-loop that are present in mammalian and plant GGTs as well as in most bacterial GGTs. Another remarkable feature of B. subtilis GGT is its salt tolerance; it retains 86% of its activity even in 3 m NaCl. To better understand these characteristics of B. subtilis GGT, we determined its crystal structure in complex with glutamate, a product of the enzymatic reaction, at 1.95 A resolution. This structure revealed that, unlike the E. coli and H. pylori GGTs, the catalytic pocket of B. subtilis GGT has no segment that covers the bound glutamate; consequently, the glutamate is exposed to solvent. Furthermore, calculation of the electrostatic potential showed that strong acidic patches were distributed on the surface of the B. subtilis GGT, even under high-salt conditions, and this may allow the protein to remain in the hydrated state and avoid self-aggregation. The structural findings presented here have implications for the molecular mechanism of GGT.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase large chain
A, C
384Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ggt
EC: 3.4.19.13
Find proteins for P54422 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P54422
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase small chain
B, D
185Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ggt
EC: 3.4.19.13
Find proteins for P54422 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P54422
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
B, D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.400α = 90.00
b = 98.890β = 90.00
c = 227.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
MOLREPphasing
BSSdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-14 
  • Released Date: 2010-03-09 
  • Deposition Author(s): Wada, K., Fukuyama, K.

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance