3FNM

Crystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals critical roles for its C-terminus in autoprocessing and catalysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Acivicin-Inhibited gamma-Glutamyltranspeptidase Reveals Critical Roles for Its C-Terminus in Autoprocessing and Catalysis.

Williams, K.Cullati, S.Sand, A.Biterova, E.I.Barycki, J.J.

(2009) Biochemistry 48: 2459-2467

  • DOI: 10.1021/bi8014955

  • PubMed Abstract: 
  • Helicobacter pylori gamma-glutamyltranspeptidase (HpGT) is a general gamma-glutamyl hydrolase and a demonstrated virulence factor. The enzyme confers a growth advantage to the bacterium, providing essential amino acid precursors by initiating the deg ...

    Helicobacter pylori gamma-glutamyltranspeptidase (HpGT) is a general gamma-glutamyl hydrolase and a demonstrated virulence factor. The enzyme confers a growth advantage to the bacterium, providing essential amino acid precursors by initiating the degradation of extracellular glutathione and glutamine. HpGT is a member of the N-terminal nucleophile (Ntn) hydrolase superfamily and undergoes autoprocessing to generate the active form of the enzyme. Acivicin is a widely used gamma-glutamyltranspeptidase inhibitor that covalently modifies the enzyme, but its precise mechanism of action remains unclear. The time-dependent inactivation of HpGT exhibits a hyperbolic dependence on acivicin concentration with k(max) = 0.033 +/- 0.006 s(-1) and K(I) = 19.7 +/- 7.2 microM. Structure determination of acivicin-modified HpGT (1.7 A; R(factor) = 17.9%; R(free) = 20.8%) demonstrates that acivicin is accommodated within the gamma-glutamyl binding pocket of the enzyme. The hydroxyl group of Thr 380, the catalytic nucleophile in the autoprocessing and enzymatic reactions, displaces chloride from the acivicin ring to form the covalently linked complex. Within the acivicin-modified HpGT structure, the C-terminus of the protein becomes ordered with Phe 567 positioned over the active site. Substitution or deletion of Phe 567 leads to a >10-fold reduction in enzymatic activity, underscoring its importance in catalysis. The mobile C-terminus is positioned by several electrostatic interactions within the C-terminal region, most notably a salt bridge between Arg 475 and Glu 566. Mutational analysis reveals that Arg 475 is critical for the proper placement of the C-terminal region, the Tyr 433 containing loop, and the proposed oxyanion hole.


    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 (Ggt) Large subunit
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 (Ggt) Small subunit
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AVN
Query on AVN

Download SDF File 
Download CCD File 
B, D
(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID
ACIVICIN
C5 H7 Cl N2 O3
QAWIHIJWNYOLBE-OKKQSCSOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AVNKi: 19700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.711α = 90.00
b = 105.376β = 91.69
c = 91.927γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SOLOMONphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-05-09
    Type: Other
  • Version 1.3: 2017-11-01
    Type: Refinement description