2PTZ

Crystal Structure of the T. brucei enolase complexed with phosphonoacetohydroxamate (PAH), His156-out conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1111/j.1742-4658.2007.06027.x
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enolase
A
432Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 1 
EC: 4.2.1.11
Find proteins for Q38BV6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q38BV6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PAH
Query on PAH

Download SDF File 
Download CCD File 
A
PHOSPHONOACETOHYDROXAMIC ACID
C2 H6 N O5 P
LDKRAXXVBWHMRH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PAHKi: 15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.858α = 90.00
b = 109.279β = 90.00
c = 107.946γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
MAR345dtbdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance