1FA5

CRYSTAL STRUCTURE OF THE ZN(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation.

He, M.M.Clugston, S.L.Honek, J.F.Matthews, B.W.

(2000) Biochemistry 39: 8719-8727

  • DOI: https://doi.org/10.1021/bi000856g
  • Primary Citation of Related Structures:  
    1F9Z, 1FA5, 1FA6, 1FA7, 1FA8

  • PubMed Abstract: 

    The metalloenzyme glyoxalase I (GlxI) converts the nonenzymatically produced hemimercaptal of cytotoxic methylglyoxal and glutathione to nontoxic S-D-lactoylglutathione. Human GlxI, for which the structure is known, is active in the presence of Zn(2+). Unexpectedly, the Escherichia coli enzyme is inactive in the presence of Zn(2+) and is maximally active with Ni(2+). To understand this difference in metal activation and also to obtain a representative of the bacterial enzymes, the structure of E. coli Ni(2+)-GlxI has been determined. Structures have also been determined for the apo enzyme as well as complexes with Co(2+), Cd(2+), and Zn(2+). It is found that each of the protein-metal complexes that is catalytically active has octahedral geometry. This includes the complexes of the E. coli enzyme with Ni(2+), Co(2+), and Cd(2+), as well as the structures reported for the human Zn(2+) enzyme. Conversely, the complex of the E. coli enzyme with Zn(2+) has trigonal bipyramidal coordination and is inactive. This mode of coordination includes four protein ligands plus a single water molecule. In contrast, the coordination in the active forms of the enzyme includes two water molecules bound to the metal ion, suggesting that this may be a key feature of the catalytic mechanism. A comparison of the human and E. coli enzymes suggests that there are differences between the active sites that might be exploited for therapeutic use.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Institute of Molecular Biology, Department of Physics, 1229 University of Oregon, Eugene, Oregon 97403-1229, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYOXALASE I
A, B
135Escherichia coliMutation(s): 0 
EC: 4.4.1.5
UniProt
Find proteins for P0AC81 (Escherichia coli (strain K12))
Explore P0AC81 
Go to UniProtKB:  P0AC81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC81
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.24α = 90
b = 57.17β = 95.36
c = 46.99γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Experimental preparation
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations