9EPN

Crystal structure of HprS histidine kinase cytoplasmic fragment from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural and biophysical characterization of the cytoplasmic domains of HprS kinase and its interactions with the cognate regulator HprR.

Koczurowska, A.Carrillo, D.R.Alai, M.G.Zaklos-Szyda, M.Bujacz, G.Pietrzyk-Brzezinska, A.J.

(2024) Arch Biochem Biophys 764: 110269-110269

  • DOI: https://doi.org/10.1016/j.abb.2024.110269
  • Primary Citation of Related Structures:  
    9EPN

  • PubMed Abstract: 

    The HprSR constitutes the bacterial two-component regulatory system engaged by Escherichia coli to reduce the damaging effects of reactive chlorine and oxygen species present in its cytosol. Hypochlorous acid (HOCl) has been shown to be the molecule capable of activating of the HprSR system. HOCl is produced upon pathogen invasion by phagocytic cells of the human innate immune system, particularly neutrophils, to take advantage of its powerful antimicrobial attributes. Therefore, comprehensive studies concerning bacterial sensing and regulatory HprSR system are indispensable in understanding and effectively eliminating pathogens. Here we present the first crystal structure, solved at 1.7 Å resolution, of the HprS cytoplasmic domains arranged as a homodimer. In both protomers, the catalytic ATP-binding domain contains a non-hydrolysable ATP analog coordinated by a magnesium ion. This structure allowed us to provide a detailed characterization of kinase-substrate interaction. Furthermore, the structural data are supported by biophysical studies of kinase interaction with cognate response regulator HprR and substrate ATP. The kinase activity is also assessed in the presence or absence of HprR.


  • Organizational Affiliation

    Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, 90-537, Lodz, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sensor histidine kinase HprS
A, B
277Escherichia coli K-12Mutation(s): 0 
Gene Names: hprSyedVb1968JW1951
EC: 2.7.13.3
UniProt
Find proteins for P76339 (Escherichia coli (strain K12))
Explore P76339 
Go to UniProtKB:  P76339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76339
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
C [auth A],
T [auth B]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
GCH
Query on GCH

Download Ideal Coordinates CCD File 
E [auth A],
V [auth B]
GLYCOCHOLIC ACID
C26 H43 N O6
RFDAIACWWDREDC-FRVQLJSFSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
L [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.89α = 90
b = 92.51β = 90
c = 118.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release