1FRO

HUMAN GLYOXALASE I WITH BENZYL-GLUTATHIONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.

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

(1997) EMBO J. 16: 3386-3395

  • DOI: 10.1093/emboj/16.12.3386

  • PubMed Abstract: 
  • The zinc metalloenzyme glyoxalase I catalyses the glutathione-dependent inactivation of toxic methylglyoxal. The structure of the dimeric human enzyme in complex with S-benzyl-glutathione has been determined by multiple isomorphous replacement (MIR) ...

    The zinc metalloenzyme glyoxalase I catalyses the glutathione-dependent inactivation of toxic methylglyoxal. The structure of the dimeric human enzyme in complex with S-benzyl-glutathione has been determined by multiple isomorphous replacement (MIR) and refined at 2.2 A resolution. Each monomer consists of two domains. Despite only low sequence homology between them, these domains are structurally equivalent and appear to have arisen by a gene duplication. On the other hand, there is no structural homology to the 'glutathione binding domain' found in other glutathione-linked proteins. 3D domain swapping of the N- and C-terminal domains has resulted in the active site being situated in the dimer interface, with the inhibitor and essential zinc ion interacting with side chains from both subunits. Two structurally equivalent residues from each domain contribute to a square pyramidal coordination of the zinc ion, rarely seen in zinc enzymes. Comparison of glyoxalase I with other known structures shows the enzyme to belong to a new structural family which includes the Fe2+-dependent dihydroxybiphenyl dioxygenase and the bleomycin resistance protein. This structural family appears to allow members to form with or without domain swapping.


    Organizational Affiliation

    Department of Molecular Biology, Uppsala University, Biomedical Center, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LACTOYLGLUTATHIONE LYASE
A, B, C, D
183Homo sapiensGene Names: GLO1
EC: 4.4.1.5
Find proteins for Q04760 (Homo sapiens)
Go to Gene View: GLO1
Go to UniProtKB:  Q04760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSB
Query on GSB

Download SDF File 
Download CCD File 
A, B, C, D
S-BENZYL-GLUTATHIONE
C17 H23 N3 O6 S
XYJWEQWNNKNSFU-STQMWFEESA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 68.000α = 90.00
b = 68.000β = 90.00
c = 169.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance