2J24

The functional role of the conserved active site proline of triosephosphate isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Functional Role of the Conserved Active Site Proline of Triosephosphate Isomerase.

Casteleijn, M.G.Alahuhta, M.Groebel, K.El-Sayed, I.Augustyns, K.Lambeir, A.M.Neubauer, P.Wierenga, R.K.

(2006) Biochemistry 45: 15483

  • DOI: https://doi.org/10.1021/bi061683j
  • Primary Citation of Related Structures:  
    2J24, 2J27

  • PubMed Abstract: 

    The importance of the fully conserved active site proline, Pro168, for the reaction mechanism of triosephosphate isomerase (TIM) has been investigated by studying the enzymatic and crystallographic properties of the P168A variant of trypanosomal TIM. In TIM, Pro168 follows the key catalytic residue Glu167, situated at the beginning of the flexible active site loop (loop 6). Turnover numbers of the P168A variant for its substrates are reduced approximately 50-fold, whereas the Km values are approximately 2 times lower. The affinity of the P168A variant for the transition state analogue 2-phosphoglycolate (2PG) is reduced 5-fold. The crystal structures of unliganded and liganded (2PG) P168A show that the phosphate moiety of 2PG is bound similarly as in wild-type TIM, whereas the interactions of the carboxylic acid moiety with the side chain of the catalytic Glu167 differ. The unique properties of the proline side chain at position 168 are required to transmit ligand binding to the conformational change of Glu167: the side chain of Glu167 flips from the inactive swung-out to the active swung-in conformation on ligand binding in wild-type TIM, whereas in the mutant this conformational change does not occur. Further structural comparisons show that in the wild-type enzyme the concerted movement of loop 6 and loop 7 from unliganded-open to liganded-closed appears to be facilitated by the interactions of the phosphate moiety with loop 7. Apparently, the rotation of 90 degrees of the Gly211-Gly212 peptide plane of loop 7 plays a key role in this concerted movement.


  • Organizational Affiliation

    Department of Process and Environmental Engineering and Bioprocess Engineering Laboratory, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
A, B
250Trypanosoma brucei bruceiMutation(s): 1 
EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei)
Explore P04789 
Go to UniProtKB:  P04789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04789
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.5α = 80.49
b = 43.72β = 79.61
c = 71.27γ = 64.66
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description