1JB1

Lactobacillus casei HprK/P Bound to Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain.

Fieulaine, S.Morera, S.Poncet, S.Monedero, V.Gueguen-Chaignon, V.Galinier, A.Janin, J.Deutscher, J.Nessler, S.

(2001) EMBO J 20: 3917-3927

  • DOI: https://doi.org/10.1093/emboj/20.15.3917
  • Primary Citation of Related Structures:  
    1JB1

  • PubMed Abstract: 

    HPr kinase/phosphatase (HprK/P) is a key regulatory enzyme controlling carbon metabolism in Gram- positive bacteria. It catalyses the ATP-dependent phosphorylation of Ser46 in HPr, a protein of the phosphotransferase system, and also its dephosphorylation. HprK/P is unrelated to eukaryotic protein kinases, but contains the Walker motif A characteristic of nucleotide-binding proteins. We report here the X-ray structure of an active fragment of Lactobacillus casei HprK/P at 2.8 A resolution, solved by the multiwavelength anomalous dispersion method on a seleniated protein (PDB code 1jb1). The protein is a hexamer, with each subunit containing an ATP-binding domain similar to nucleoside/nucleotide kinases, and a putative HPr-binding domain unrelated to the substrate-binding domains of other kinases. The Walker motif A forms a typical P-loop which binds inorganic phosphate in the crystal. We modelled ATP binding by comparison with adenylate kinase, and designed a tentative model of the complex with HPr based on a docking simulation. The results confirm that HprK/P represents a new family of protein kinases, first identified in bacteria, but which may also have members in eukaryotes.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063, CNRS, 91198 Gif sur Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HPRK PROTEIN205Lacticaseibacillus caseiMutation(s): 4 
Gene Names: PTSK
EC: 2.7.1 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt
Find proteins for Q9RE09 (Lacticaseibacillus casei)
Explore Q9RE09 
Go to UniProtKB:  Q9RE09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RE09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.738α = 90
b = 107.738β = 90
c = 66.498γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
MADSYSphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description