2QMC

Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase T380A Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of Helicobacter pylori gamma-glutamyltranspeptidase reveals the molecular basis for substrate specificity and a critical role for the tyrosine 433-containing loop in catalysis.

Morrow, A.L.Williams, K.Sand, A.Boanca, G.Barycki, J.J.

(2007) Biochemistry 46: 13407-13414

  • DOI: 10.1021/bi701599e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Helicobacter pylori gamma-glutamyltranspeptidase (HpGT) is a member of the N-terminal nucleophile hydrolase superfamily. It is translated as an inactive 60 kDa polypeptide precursor that undergoes intramolecular autocatalytic cleavage to generate a f ...

    Helicobacter pylori gamma-glutamyltranspeptidase (HpGT) is a member of the N-terminal nucleophile hydrolase superfamily. It is translated as an inactive 60 kDa polypeptide precursor that undergoes intramolecular autocatalytic cleavage to generate a fully active heterodimer composed of a 40 kDa and a 20 kDa subunit. The resultant N-terminus, Thr 380, has been shown to be the catalytic nucleophile in both autoprocessing and enzymatic reactions. Once processed, HpGT catalyzes the hydrolysis of the gamma-glutamyl bond in glutathione and its conjugates. To facilitate the determination of physiologically relevant substrates for the enzyme, crystal structures of HpGT in complex with glutamate (1.6 A, Rfactor = 16.7%, Rfree = 19.0%) and an inactive HpGT mutant, T380A, in complex with S-(nitrobenzyl)glutathione (1.55 A, Rfactor = 18.7%, Rfree = 21.8%) have been determined. Residues that comprise the gamma-glutamyl binding site are primarily located in the 20 kDa subunit and make numerous hydrogen bonds with the alpha-amino and alpha-carboxylate groups of the substrate. In contrast, a single hydrogen bond occurs between the T380A mutant and the remainder of the ligand. Lack of specific coordination beyond the gamma-glutamyl moiety may account for the substrate binding permissiveness of the enzyme. Structural analysis was combined with site-directed mutagenesis of residues involved in maintaining the conformation of a loop region that covers the gamma-glutamyl binding site. Results provide evidence that access to this buried site may occur through conformational changes in the Tyr 433-containing loop, as disruption of the intricate hydrogen-bond network responsible for optimal placement of Tyr 433 significantly diminishes catalytic activity.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biochemistry, University of Nebraska, 1901 Vine Street, Lincoln, Nebraska 68588-0664, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-glutamyltranspeptidase
A, C
377Helicobacter 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): 1 
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25743
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTB
Query on GTB

Download SDF File 
Download CCD File 
B, D
S-(P-NITROBENZYL)GLUTATHIONE
C17 H22 N4 O8 S
OAWORKDPTSAMBZ-STQMWFEESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.140α = 90.00
b = 106.674β = 104.96
c = 87.194γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description