2IE8

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.209 

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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
  • Primary Citation of Related Structures:  
    2IE8

  • 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 change occurs that brings the N- and C-domains of PGK closer together ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoglycerate kinaseA390Thermus caldophilusMutation(s): 0 
Gene Names: pgk
EC: 2.7.2.3
UniProt
Find proteins for Q08GC7 (Thermus caldophilus)
Explore Q08GC7 
Go to UniProtKB:  Q08GC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08GC7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.1α = 90
b = 71.3β = 90
c = 80.2γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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