1FW8

CIRCULARLY PERMUTED PHOSPHOGLYCERATE KINASE FROM YEAST: PGK P72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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.,Sect.D 58: 2018-2023


  • 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 direct ...

    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.


    Related Citations: 
    • Is the continuity of the domains required for the correct folding of a two-domain protein?
      Ritco-Vonsovici, M.,Minard, P.,Desmadril, M.,Yon, J.M.
      (1995) Biochemistry 34: 16543


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoglycerate kinase
A
416Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PGK1
EC: 2.7.2.3
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PGK1
Go to UniProtKB:  P00560
Small Molecules
Ligands 1 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.740α = 90.00
b = 104.770β = 90.00
c = 44.340γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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