X-ray structure of the HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.226 

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Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions.

Marquez, J.A.Hasenbein, S.Koch, B.Fieulaine, S.Nessler, S.Russell, R.B.Hengstenberg, W.Scheffzek, K.

(2002) Proc Natl Acad Sci U S A 99: 3458-3463

  • DOI: https://doi.org/10.1073/pnas.052461499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The histidine containing phospho carrier protein (HPr) kinase/phosphatase is involved in carbon catabolite repression, mainly in Gram-positive bacteria. It is a bifunctional enzyme that phosphorylates Ser-46-HPr in an ATP-dependent reaction and dephosphorylates P-Ser-46-HPr. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The N-terminal domain has a betaalphabeta fold similar to a segment from enzyme I of the sugar phosphotransferase system and to the uridyl-binding portion of MurF; it is structurally organized in three dimeric modules exposed to form the propeller blades. Two unexpected phosphate ions associated with highly conserved residues were found in the N-terminal dimeric interface. The C-terminal kinase domain is similar to that of the Lactobacillus casei enzyme and is assembled in six copies to form the compact central hub of the propeller. Beyond previously reported similarity with adenylate kinase, we suggest evolutionary relationship with phosphoenolpyruvate carboxykinase. In addition to a phosphate ion in the phosphate-binding loop of the kinase domain, we have identified a second phosphate-binding site that, by comparison with adenylate kinases, we believe accommodates a product/substrate phosphate, normally covalently linked to Ser-46 of HPr. Thus, we propose that our structure represents a product/substrate mimic of the kinase/phosphatase reaction.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Programme, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hpr kinase/phosphatase
A, B
314Staphylococcus xylosusMutation(s): 0 
Gene Names: HPRK
EC: 2.7.1 (PDB Primary Data), 3.1.3 (PDB Primary Data)
Find proteins for Q9S1H5 (Staphylococcus xylosus)
Explore Q9S1H5 
Go to UniProtKB:  Q9S1H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S1H5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.226 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.24α = 90
b = 152.24β = 90
c = 194.686γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-03
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description