2PU1

Crystal Structure of the T. brucei enolase complexed with Fluoro-phosphonoacetohydroxamate (FPAH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics.

Navarro, M.V.Gomes Dias, S.M.Mello, L.V.da Silva Giotto, M.T.Gavalda, S.Blonski, C.Garratt, R.C.Rigden, D.J.

(2007) FEBS J 274: 5077-5089

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.06027.x
  • Primary Citation of Related Structures:  
    2PTW, 2PTX, 2PTY, 2PTZ, 2PU0, 2PU1

  • PubMed Abstract: 

    Enolase is a validated drug target in Trypanosoma brucei. To better characterize its properties and guide drug design efforts, we have determined six new crystal structures of the enzyme, in various ligation states and conformations, and have carried out complementary molecular dynamics simulations. The results show a striking structural diversity of loops near the catalytic site, for which variation can be interpreted as distinct modes of conformational variability that are explored during the molecular dynamics simulations. Our results show that sulfate may, unexpectedly, induce full closure of catalytic site loops whereas, conversely, binding of inhibitor phosphonoacetohydroxamate may leave open a tunnel from the catalytic site to protein surface offering possibilities for drug development. We also present the first complex of enolase with a novel inhibitor 2-fluoro-2-phosphonoacetohydroxamate. The molecular dynamics results further encourage efforts to design irreversible species-specific inhibitors: they reveal that a parasite enzyme-specific lysine may approach the catalytic site more closely than crystal structures suggest and also cast light on the issue of accessibility of parasite enzyme-specific cysteines to chemically modifying reagents. One of the new sulfate structures contains a novel metal-binding site IV within the catalytic site cleft.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enolase432Trypanosoma bruceiMutation(s): 1 
EC: 4.2.1.11
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.809α = 90
b = 110.644β = 90
c = 109.006γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description