4Y23

Crystal structure of T399A precursor mutant protein of gamma-glutamyl transpeptidase from Bacillus licheniformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The maturation mechanism of gamma-glutamyl transpeptidases: Insights from the crystal structure of a precursor mimic of the enzyme from Bacillus licheniformis and from site-directed mutagenesis studies.

Pica, A.Chi, M.C.Chen, Y.Y.d'Ischia, M.Lin, L.L.Merlino, A.

(2015) Biochim.Biophys.Acta 1864: 195-203

  • DOI: 10.1016/j.bbapap.2015.10.006

  • PubMed Abstract: 
  • γ-Glutamyl transpeptidases (γ-GTs) are members of N-terminal nucleophile hydrolase superfamily. They are synthetized as single-chain precursors, which are then cleaved to form mature enzymes. Basic aspects of autocatalytic processing of these pro-enz ...

    γ-Glutamyl transpeptidases (γ-GTs) are members of N-terminal nucleophile hydrolase superfamily. They are synthetized as single-chain precursors, which are then cleaved to form mature enzymes. Basic aspects of autocatalytic processing of these pro-enzymes are still unknown. Here we describe the X-ray structure of the precursor mimic of Bacillus licheniformis γ-GT (BlGT), obtained by mutating catalytically important threonine to alanine (T399A-BlGT), and report results of autoprocessing of mutants of His401, Thr415, Thr417, Glu419 and Arg571. Data suggest that Thr417 is in a competent position to activate the catalytic threonine (Thr399) for nucleophilic attack of the scissile peptide bond and that Thr415 plays a major role in assisting the process. On the basis of these new structural results, a possible mechanism of autoprocessing is proposed. This mechanism, which guesses the existence of a six-membered transition state involving one carbonyl and two hydroxyl groups, is in agreement with all the available experimental data collected on γ-GTs from different species and with our new Ala-scanning mutagenesis data.


    Organizational Affiliation

    Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone, 16, Naples 80133, Italy. Electronic address: antonello.merlino@unina.it.,Department of Applied Chemistry, National Chiayi University, 300 Syuefu Road, Chiayi City 60004, Taiwan.,Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Naples I-80126, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma glutamyl transpeptidase,Gamma-glutamyltranspeptidase
A
585Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)Mutation(s): 1 
Gene Names: ggt
Find proteins for Q65KZ6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46))
Go to UniProtKB:  Q65KZ6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.438α = 90.00
b = 59.438β = 90.00
c = 281.930γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-02-09 
  • Released Date: 2015-11-18 
  • Deposition Author(s): Pica, A., Merlino, A.

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Database references