Structure of Trypanosoma brucei enolase reveals the inhibitory divalent metal site

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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The Crystal Structure of Trypanosoma Brucei Enolase: Visualisation of the Inhibitory Metal Binding Site III and Potential as Target for Selective, Irreversible Inhibition

Da Silva Giotto, M.T.Hannaert, V.Vertommen, D.Navarro, M.V.A.S.Rider, M.H.Michels, P.A.M.Garratt, R.C.Rigden, D.J.

(2003) J Mol Biol 331: 653

  • DOI: https://doi.org/10.1016/s0022-2836(03)00752-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The glycolytic enzymes of the trypanosomatids, that cause a variety of medically and agriculturally important diseases, are validated targets for drug design. Design of species-specific inhibitors is facilitated by the availability of structural data. Irreversible inhibitors, that bound covalently to the parasite enzyme alone, would be potentially particularly effective. Here we determine the crystal structure of enolase from Trypanosoma brucei and show that two cysteine residues, located in a water-filled cavity near the active-site, are modified by iodoacetamide leading to loss of catalytic activity. Since these residues are specific to the Trypanosomatidae lineage, this finding opens the way for the development of parasite-specific, irreversibly binding enolase inhibitors. In the present structure, the catalytic site is partially occupied by sulphate and two zinc ions. Surprisingly, one of these zinc ions illustrates the existence of a novel enolase-binding site for divalent metals. Evidence suggests that this is the first direct visualization of the elusive inhibitory metal site, whose existence has hitherto only been inferred from kinetic data.

  • Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos SP, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENOLASE432Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q9NDH8 (Trypanosoma brucei brucei)
Explore Q9NDH8 
Go to UniProtKB:  Q9NDH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NDH8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.018α = 90
b = 110.536β = 90
c = 109.098γ = 90
Software Package:
Software NamePurpose
AUTOMARdata reduction
AUTOMARdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description