2NQO

Crystal Structure of Helicobacter pylori gamma-Glutamyltranspeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Autoprocessing of Helicobacter pylori gamma-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad.

Boanca, G.Sand, A.Okada, T.Suzuki, H.Kumagai, H.Fukuyama, K.Barycki, J.J.

(2007) J.Biol.Chem. 282: 534-541

  • DOI: 10.1074/jbc.M607694200
  • Also Cited By: 2QMC, 2QM6

  • PubMed Abstract: 
  • Helicobacter pylorigamma-glutamyltranspeptidase (HpGT) is a glutathione-degrading enzyme that has been shown to be a virulence factor in infection. It is expressed as a 60-kDa inactive precursor that must undergo autocatalytic processing to generate ...

    Helicobacter pylorigamma-glutamyltranspeptidase (HpGT) is a glutathione-degrading enzyme that has been shown to be a virulence factor in infection. It is expressed as a 60-kDa inactive precursor that must undergo autocatalytic processing to generate a 40-kDa/20-kDa heterodimer with full gamma-glutamyl amide bond hydrolase activity. The new N terminus of the processed enzyme, Thr-380, is the catalytic nucleophile in both the autoprocessing and enzymatic reactions, indicating that HpGT is a member of the N-terminal nucleophile hydrolase superfamily. To further investigate activation as a result of autoprocessing, the structure of HpGT has been determined to a resolution of 1.9 A. The refined model contains two 40-kDa/20-kDa heterodimers in the asymmetric unit and has structural features comparable with other N-terminal nucleophile hydrolases. Autoprocessing of HpGT leads to a large conformational change, with the loop preceding the catalytic Thr-380 moving >35 A, thus relieving steric constraints that likely limit substrate binding. In addition, cleavage of the proenzyme results in the formation of a threonine-threonine dyad comprised of Thr-380 and a second conserved threonine residue, Thr-398. The hydroxyl group of Thr-398 is located equidistant from the alpha-amino group and hydroxyl side chain of Thr-380. Mutation of Thr-398 to an alanine results in an enzyme that is fully capable of autoprocessing but is devoid of enzymatic activity. Substrate docking studies in combination with homology modeling studies of the human homologue reveal additional mechanistic details of enzyme maturation and activation, substrate recognition, and catalysis.


    Organizational Affiliation

    Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase
A, C
376Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25743
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase
B, D
188Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25743
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.354α = 90.00
b = 105.206β = 91.99
c = 91.060γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNSphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description