1FW8

CIRCULARLY PERMUTED PHOSPHOGLYCERATE KINASE FROM YEAST: PGK P72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a circularly permuted phosphoglycerate kinase.

Tougard, P.Bizebard, T.Ritco-Vonsovici, M.Minard, P.Desmadril, M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 2018-2023

  • DOI: https://doi.org/10.1107/s0907444902015548
  • Primary Citation of Related Structures:  
    1FW8

  • PubMed Abstract: 

    The crystallographic structure of a circularly permuted form of yeast PGK, 72p yPGK, has been determined to a resolution of 2.3 A by molecular replacement. In this engineered protein, the C- and N-terminal residues of the wild-type protein are directly connected by a peptide bond and new N- and C-terminal residues are located within the N-terminal domain. The overall fold of the protein is very similar to that of the wild-type protein, directly demonstrating that the continuity of a folding unit is not relevant to the folding process of the whole protein. Only limited structural changes were observed: these were in the regions associated with the new connection, in a long flexible loop in the permuted domain and in the vicinity of Arg38, a functionally important residue. The relative positions of the two domains suggested that this permuted protein adopts one of the most open/twisted conformations seen amongst PGKs of known structure. The effect of the mutation on the functional properties is more easily accounted for by a restriction of hinge-bending motion than by structural changes in the protein.


  • Organizational Affiliation

    Laboratoire de Modélisation et d'Ingénierie des Protéines, UMR 8619, Université de Paris-Sud, Bâtiment 430, F-91405 Orsay CEDEX, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase416Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PGK1YCR012WYCR12W
EC: 2.7.2.3
UniProt
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00560 
Go to UniProtKB:  P00560
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00560
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 104.77β = 90
c = 44.34γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Advisory, Database references, Refinement description, Source and taxonomy, Structure summary