4JGO

The crystal structure of sporulation kinase d sensor domain from Bacillus subtilis subsp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD.

Wu, R.Gu, M.Wilton, R.Babnigg, G.Kim, Y.Pokkuluri, P.R.Szurmant, H.Joachimiak, A.Schiffer, M.

(2013) Protein Sci. 22: 564-576

  • DOI: 10.1002/pro.2237
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extra ...

    The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand-binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD-dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.


    Organizational Affiliation

    The Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sporulation kinase D
A, B
217Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: kinD (ykvD)
EC: 2.7.13.3
Find proteins for O31671 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31671
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download SDF File 
Download CCD File 
A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.107α = 90.00
b = 82.533β = 90.00
c = 90.375γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release