2C21

Specificity of the Trypanothione-dependednt Leishmania major Glyoxalase I: Structure and biochemical comparison with the human enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Specificity of the Trypanothione-Dependent Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme.

Ariza, A.Vickers, T.J.Greig, N.Armour, K.A.Dixon, M.J.Eggleston, I.M.Fairlamb, A.H.Bond, C.S.

(2006) Mol Microbiol 59: 1239

  • DOI: https://doi.org/10.1111/j.1365-2958.2006.05022.x
  • Primary Citation of Related Structures:  
    2C21

  • PubMed Abstract: 

    Trypanothione replaces glutathione in defence against cellular damage caused by oxidants, xenobiotics and methylglyoxal in the trypanosomatid parasites, which cause trypanosomiasis and leishmaniasis. In Leishmania major, the first step in methylglyoxal detoxification is performed by a trypanothione-dependent glyoxalase I (GLO1) containing a nickel cofactor; all other characterized eukaryotic glyoxalases use zinc. In kinetic studies L. major and human enzymes were active with methylglyoxal derivatives of several thiols, but showed opposite substrate selectivities: N1-glutathionylspermidine hemithioacetal is 40-fold better with L. major GLO1, whereas glutathione hemithioacetal is 300-fold better with human GLO1. Similarly, S-4-bromobenzylglutathionylspermidine is a 24-fold more potent linear competitive inhibitor of L. major than human GLO1 (Kis of 0.54 microM and 12.6 microM, respectively), whereas S-4-bromobenzylglutathione is >4000-fold more active against human than L. major GLO1 (Kis of 0.13 microM and >500 microM respectively). The crystal structure of L. major GLO1 reveals differences in active site architecture to both human GLO1 and the nickel-dependent Escherichia coli GLO1, including increased negative charge and hydrophobic character and truncation of a loop that may regulate catalysis in the human enzyme. These differences correlate with the differential binding of glutathione and trypanothione-based substrates, and thus offer a route to the rational design of L. major-specific GLO1 inhibitors.


  • Organizational Affiliation

    Division of Biological Chemistry & Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRYPANOTHIONE-DEPENDENT GLYOXALASE I
A, B, C, D, E
A, B, C, D, E, F
144Leishmania majorMutation(s): 0 
EC: 4.1.1
UniProt
Find proteins for Q68RJ8 (Leishmania major)
Explore Q68RJ8 
Go to UniProtKB:  Q68RJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68RJ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth D]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
O [auth C]
P [auth D]
R [auth D]
I [auth A],
K [auth B],
O [auth C],
P [auth D],
R [auth D],
V [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
M [auth C]
N [auth C]
T [auth E]
G [auth A],
H [auth A],
M [auth C],
N [auth C],
T [auth E],
U [auth E]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth B],
S [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.193α = 90
b = 148.957β = 90
c = 50.698γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description