3WHS

Crystal structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue.

Ida, T.Suzuki, H.Fukuyama, K.Hiratake, J.Wada, K.

(2014) Acta Crystallogr.,Sect.D 70: 607-614

  • DOI: 10.1107/S1399004713031222
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å ...

    γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp2 hybridization to Thr403 Oγ, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.


    Organizational Affiliation

    Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan.,Division of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.,Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase large chain
A
418Bacillus 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
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
AVN
Query on AVN

Download SDF File 
Download CCD File 
B
(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID
ACIVICIN
C5 H7 Cl N2 O3
QAWIHIJWNYOLBE-OKKQSCSOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.075α = 90.00
b = 71.666β = 90.00
c = 144.357γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-30 
  • Released Date: 2014-02-19 
  • Deposition Author(s): Wada, K., Fukuyama, K.

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references, Derived calculations