1N55

0.83A resolution structure of the E65Q mutant of Leishmania mexicana triosephosphate isomerase complexed with 2-phosphoglycolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution

Kursula, I.Wierenga, R.K.

(2003) J Biol Chem 278: 9544-9551

  • DOI: 10.1074/jbc.M211389200
  • Primary Citation of Related Structures:  
    1N55

  • PubMed Abstract: 
  • The atomic resolution structure of Leishmania mexicana triosephosphate isomerase complexed with 2-phosphoglycolate shows that this transition state analogue is bound in two conformations. Also for the side chain of the catalytic glutamate, Glu(167), ...

    The atomic resolution structure of Leishmania mexicana triosephosphate isomerase complexed with 2-phosphoglycolate shows that this transition state analogue is bound in two conformations. Also for the side chain of the catalytic glutamate, Glu(167), two conformations are observed. In both conformations, a very short hydrogen bond exists between the carboxylate group of the ligand and the catalytic glutamate. The distance between O11 of PGA and Oepsilon2 of Glu(167) is 2.61 and 2.55 A for the major and minor conformations, respectively. In either conformation, Oepsilon1 of Glu(167) is hydrogen-bonded to a water network connecting the side chain with bulk solvent. This network also occurs in two mutually exclusive arrangements. Despite the structural disorder in the active site, the C termini of the beta strands that construct the active site display the least anisotropy compared with the rest of the protein. The loops following these beta strands display various degrees of anisotropy, with the tip of the dimer interface loop 3 having very low anisotropy and the C-terminal region of the active site loop 6 having the highest anisotropy. The pyrrolidine ring of Pro(168) at the N-terminal region of loop 6 is in a strained planar conformation to facilitate loop opening and product release.


    Organizational Affiliation

    Department of Biochemistry and Biocenter Oulu, University of Oulu, P. O. Box 3000, Oulu FIN-90014, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
triosephosphate isomeraseA251Leishmania mexicanaMutation(s): 1 
EC: 5.3.1.1
Find proteins for P48499 (Leishmania mexicana)
Explore P48499 
Go to UniProtKB:  P48499
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download CCD File 
A
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.095 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.072α = 90
b = 50.58β = 118.09
c = 58.884γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance