Crystal structure analysis of pyruvate kinase from Bacillus stearothermophilus

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 

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Crystal structure of pyruvate kinase from Geobacillus stearothermophilus.

Suzuki, K.Ito, S.Shimizu-Ibuka, A.Sakai, H.

(2008) J Biochem 144: 305-312

  • DOI: https://doi.org/10.1093/jb/mvn069
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The pyruvate kinase (PK) from a moderate thermophile, Geobacillus stearothermophilus, is an allosteric enzyme activated by AMP and ribose 5-phosphate but not fructose 1, 6-bisphosphate (FBP), which is a common activator of PKs. It has an extra C-terminal sequence (ECTS), which contains a highly conserved phosphoenolpyruvate (PEP) binding motif, but its function and structure remain unclear. To elucidate the structural characteristics of the effector-binding site and the ECTS, the crystal structure of the C9S/C268S mutant of the enzyme was determined at 2.4 A resolution. The crystal belonged to space group P6(2)22, with unit cell parameters a, b = 145.97 A, c = 118.03 A. The enzyme was a homotetramer and its overall domain structure was similar to the previously solved structures except that the ECTS formed a new domain (C' domain). The structure of the C' domain closely resembled that of the PEP binding domain of maize pyruvate phosphate dikinase. A sulphate ion was found in a pocket in the effector-binding C domain. This site corresponds to the 6-phosphate group-binding site in yeast PK bound FBP and seems to be the effector-binding site. Through comparison of the structure of the putative effector-binding site to that of the FBP binding site of the yeast enzyme, the structural basis of the effector specificity of the G. stearothermophilus PK is discussed.

  • Organizational Affiliation

    Department of Food and Nutritional Sciences, University of Shizuoka, Yada 52-1, Shizuoka 422-8526, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase587Geobacillus stearothermophilusMutation(s): 2 
Find proteins for Q02499 (Geobacillus stearothermophilus)
Explore Q02499 
Go to UniProtKB:  Q02499
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02499
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.97α = 90
b = 145.97β = 90
c = 118.03γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-02-05 
  • Deposition Author(s): Suzuki, K.

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description