2Y62

Crystal structure of Leishmanial E65Q-TIM complexed with R-Glycidol phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High Resolution Crystal Structures of Triosephosphate Isomerase Complexed with its Suicide Inhibitors: The Conformational Flexibility of the Catalytic Glutamate in its Closed, Liganded Active Site.

Venkatesan, R.Alahuhta, M.Pihko, P.M.Wierenga, R.K.

(2011) Protein Sci. 20: 1387

  • DOI: 10.1002/pro.667
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The key residue of the active site of triosephosphate isomerase (TIM) is the catalytic glutamate, which is proposed to be important (i) as a catalytic base, for initiating the reaction, as well as (ii) for the subsequent proton shuttling steps. The s ...

    The key residue of the active site of triosephosphate isomerase (TIM) is the catalytic glutamate, which is proposed to be important (i) as a catalytic base, for initiating the reaction, as well as (ii) for the subsequent proton shuttling steps. The structural properties of this glutamate in the liganded complex have been investigated by studying the high resolution crystal structures of typanosomal TIM, complexed with three suicide inhibitors: (S)-glycidol phosphate ((S)-GOP, at 0.99 Å resolution), (R)-glycidol phosphate, ((R)-GOP, at 1.08 Å resolution), and bromohydroxyacetone phosphate (BHAP, at 1.97 Å resolution). The structures show that in the (S)-GOP active site this catalytic glutamate is in the well characterized, competent conformation. However, an unusual side chain conformation is observed in the (R)-GOP and BHAP complexes. In addition, Glu97, salt bridged to the catalytic lysine in the competent active site, adopts an unusual side chain conformation in these two latter complexes. The higher chemical reactivity of (S)-GOP compared with (R)-GOP, as known from solution studies, can be understood: the structures indicate that in the case of (S)-GOP, Glu167 can attack the terminal carbon of the epoxide in a stereoelectronically favored, nearly linear OCO arrangement, but this is not possible for the (R)-GOP isomer. These structures confirm the previously proposed conformational flexibility of the catalytic glutamate in its closed, liganded state. The importance of this conformational flexibility for the proton shuttling steps in the TIM catalytic cycle, which is apparently achieved by a sliding motion of the side chain carboxylate group above the enediolate plane, is also discussed.


    Organizational Affiliation

    Biocenter Oulu and Department of Biochemistry, University of Oulu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM
A
251Leishmania mexicanaMutation(s): 1 
EC: 5.3.1.1
Find proteins for P48499 (Leishmania mexicana)
Go to UniProtKB:  P48499
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
G3P
Query on G3P

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Download CCD File 
A
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
 Ligand Interaction
1GP
Query on 1GP

Download SDF File 
Download CCD File 
A
SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.760α = 90.00
b = 52.460β = 118.08
c = 58.250γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXL-97refinement
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release