4Y23 | pdb_00004y23

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 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1016/j.bbapap.2015.10.006
  • Primary Citation Related Structures: 
    4Y23

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 64.09 kDa 
  • Atom Count: 4,267 
  • Modeled Residue Count: 550 
  • Deposited Residue Count: 585 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma glutamyl transpeptidase,Gamma-glutamyltranspeptidase585Bacillus licheniformisMutation(s): 1 
EC: 2.3.2.2 (PDB Primary Data), 3.4.19.13 (UniProt)
UniProt
Find proteins for Q65KZ6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65KZ6 
Go to UniProtKB:  Q65KZ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65KZ6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.438α = 90
b = 59.438β = 90
c = 281.93γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description