2E28

Crystal structure analysis of pyruvate kinase from Bacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of pyruvate kinase from Geobacillus stearothermophilus.

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

(2008) J.Biochem. 144: 305-312

  • DOI: 10.1093/jb/mvn069

  • 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-term ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase
A
587Geobacillus stearothermophilusMutation(s): 2 
Gene Names: pyk
EC: 2.7.1.40
Find proteins for Q02499 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q02499
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 145.970α = 90.00
b = 145.970β = 90.00
c = 118.030γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-09 
  • Released Date: 2008-02-05 
  • Deposition Author(s): Suzuki, K.

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance