Crystal structure of psychrophilic phosphoglycerate kinase from Pseudomonas TACII18 in complex with 3-phosphoglycerate

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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Structural determinants increasing flexibility confer cold adaptation in psychrophilic phosphoglycerate kinase.

Mandelman, D.Ballut, L.Wolff, D.A.Feller, G.Gerday, C.Haser, R.Aghajari, N.

(2019) Extremophiles 23: 495-506

  • DOI: https://doi.org/10.1007/s00792-019-01102-x
  • Primary Citation of Related Structures:  
    6HXE, 6I06

  • PubMed Abstract: 

    Crystal structures of phosphoglycerate kinase (PGK) from the psychrophile Pseudomonas sp. TACII 18 have been determined at high resolution by X-ray crystallography methods and compared with mesophilic, thermophilic and hyperthermophilic counterparts. PGK is a two-domain enzyme undergoing large domain movements to catalyze the production of ATP from 1,3-biphosphoglycerate and ADP. Whereas the conformational dynamics sustaining the catalytic mechanism of this hinge-bending enzyme now seems rather clear, the determinants which underlie high catalytic efficiency at low temperatures of this psychrophilic PGK were unknown. The comparison of the three-dimensional structures shows that multiple (global and local) specific adaptations have been brought about by this enzyme. Together, these reside in an overall increased flexibility of the cold-adapted PGK thereby allowing a better accessibility to the active site, but also a potentially more disordered transition state of the psychrophilic enzyme, due to the destabilization of some catalytic residues.

  • Organizational Affiliation

    Biocrystallography and Structural Biology of Therapeutic Targets, Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase387Pseudomonas sp. 'TAC II 18Mutation(s): 0 
Gene Names: pgk
Find proteins for Q9RBS3 (Pseudomonas sp. 'TAC II 18')
Explore Q9RBS3 
Go to UniProtKB:  Q9RBS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RBS3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3PG

Download Ideal Coordinates CCD File 
C3 H7 O7 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.5α = 90
b = 58.5β = 90
c = 85.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European UnionFranceCT970131

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description