1JB1

Lactobacillus casei HprK/P Bound to Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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: 10.1093/emboj/20.15.3917

  • 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 dephosphoryl ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HPRK PROTEIN
A
205Lactobacillus caseiGene Names: hprK
EC: 2.7.11.-, 2.7.4.-
Find proteins for Q9RE09 (Lactobacillus casei)
Go to UniProtKB:  Q9RE09
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 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 = 90.00
b = 107.738β = 90.00
c = 66.498γ = 120.00
Software Package:
Software NamePurpose
MADSYSphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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