1QH3 | pdb_00001qh3

HUMAN GLYOXALASE II WITH CACODYLATE AND ACETATE IONS PRESENT IN THE ACTIVE SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.239 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QH3

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue.

Cameron, A.D.Ridderstrom, M.Olin, B.Mannervik, B.

(1999) Structure 7: 1067-1078

  • DOI: https://doi.org/10.1016/s0969-2126(99)80174-9
  • Primary Citation Related Structures: 
    1QH3, 1QH5

  • PubMed Abstract: 

    Glyoxalase II, the second of two enzymes in the glyoxalase system, is a thiolesterase that catalyses the hydrolysis of S-D-lactoylglutathione to form glutathione and D-lactic acid. The structure of human glyoxalase II was solved initially by single isomorphous replacement with anomalous scattering and refined at a resolution of 1.9 A. The enzyme consists of two domains. The first domain folds into a four-layered beta sandwich, similar to that seen in the metallo-beta-lactamases. The second domain is predominantly alpha-helical. The active site contains a binuclear zinc-binding site and a substrate-binding site extending over the domain interface. The model contains acetate and cacodylate in the active site. A second complex was derived from crystals soaked in a solution containing the slow substrate, S-(N-hydroxy-N-bromophenylcarbamoyl)glutathione. This complex was refined at a resolution of 1.45 A. It contains the added ligand in one molecule of the asymmetric unit and glutathione in the other. The arrangement of ligands around the zinc ions includes a water molecule, presumably in the form of a hydroxide ion, coordinated to both metal ions. This hydroxide ion is situated 2.9 A from the carbonyl carbon of the substrate in such a position that it could act as the nucleophile during catalysis. The reaction mechanism may also have implications for the action of metallo-beta-lactamases.


  • Organizational Affiliation
    • Department of Molecular Biology Uppsala University Biomedical Center Box 590, S-751 24, Uppsala, Sweden Structural Biology Laboratory Department of Chemistry University of York Heslington, York, UK YO10 5DD,. cameron@yorvic.york.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 58.88 kDa 
  • Atom Count: 4,452 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
A, B
260Homo sapiensMutation(s): 0 
EC: 3.1.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q16775 (Homo sapiens)
Explore Q16775 
Go to UniProtKB:  Q16775
PHAROS:  Q16775
GTEx:  ENSG00000063854 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16775
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC

Query on CAC



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A],
L [auth B],
N [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN

Query on MN



Download:Ideal Coordinates CCD File
H [auth A],
O [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.239 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.08α = 90
b = 72.37β = 90
c = 162.06γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations