3IBH | pdb_00003ibh

Crystal structure of Saccharomyces cerevisiae Gtt2 in complex with glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structures of yeast glutathione-S-transferase Gtt2 reveal a new catalytic type of GST family.

Ma, X.X.Jiang, Y.L.He, Y.X.Bao, R.Chen, Y.X.Zhou, C.Z.

(2009) EMBO Rep 10: 1320-1326

  • DOI: https://doi.org/10.1038/embor.2009.216
  • Primary Citation Related Structures: 
    3ERF, 3ERG, 3IBH

  • PubMed Abstract: 

    Glutathione-S-transferases (GSTs) are ubiquitous detoxification enzymes that catalyse the conjugation of electrophilic substrates to glutathione. Here, we present the crystal structures of Gtt2, a GST of Saccharomyces cerevisiae, in apo and two ligand-bound forms, at 2.23 A, 2.20 A and 2.10 A, respectively. Although Gtt2 has the overall structure of a GST, the absence of the classic catalytic essential residues--tyrosine, serine and cysteine--distinguishes it from all other cytosolic GSTs of known structure. Site-directed mutagenesis in combination with activity assays showed that instead of the classic catalytic residues, a water molecule stabilized by Ser129 and His123 acts as the deprotonator of the glutathione sulphur atom. Furthermore, only glycine and alanine are allowed at the amino-terminus of helix-alpha1 because of stereo-hindrance. Taken together, these results show that yeast Gtt2 is a novel atypical type of cytosolic GST.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 26.68 kDa 
  • Atom Count: 1,789 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 233 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Saccharomyces cerevisiae Gtt2233Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GTT2L0560YLL060C
EC: 2.5.1.18
UniProt
Find proteins for Q12390 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12390 
Go to UniProtKB:  Q12390
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12390
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on GSH



Download:Ideal Coordinates CCD File
B [auth A]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.774α = 90
b = 88.774β = 90
c = 69.102γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Non-polymer description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description