2IE8

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

Lee, J.H.Im, Y.J.Bae, J.Kim, D.Kim, M.K.Kang, G.B.Lee, D.S.Eom, S.H.

(2006) Biochem.Biophys.Res.Commun. 350: 1044-1049

  • DOI: 10.1016/j.bbrc.2006.09.151

  • PubMed Abstract: 
  • Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational cha ...

    Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational change occurs that brings the N- and C-domains of PGK closer together. Here we present the 1.8A crystal structure of unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK (closed conformation) revealed that the conformational change reflects a change in the interaction between the domains. We identified Arg148 as a key residue involved in open-to-closed transition. The open conformation of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation.


    Organizational Affiliation

    Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoglycerate kinase
A
390Thermus caldophilusMutation(s): 0 
Gene Names: pgk
EC: 2.7.2.3
Find proteins for Q08GC7 (Thermus caldophilus)
Go to UniProtKB:  Q08GC7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.100α = 90.00
b = 71.300β = 90.00
c = 80.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
ADSCdata collection
SCALEPACKdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance