3D36 | pdb_00003d36

How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus KinB with the Inhibitor Sda


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.215 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

How to switch off a histidine kinase: crystal structure of Geobacillus stearothermophilus KinB with the inhibitor Sda

Bick, M.J.Lamour, V.Rajashankar, K.R.Gordiyenko, Y.Robinson, C.V.Darst, S.A.

(2009) J Mol Biology 386: 163-177

  • DOI: https://doi.org/10.1016/j.jmb.2008.12.006
  • Primary Citation Related Structures: 
    3D36

  • PubMed Abstract: 

    Entry to sporulation in bacilli is governed by a histidine kinase phosphorelay, a variation of the predominant signal transduction mechanism in prokaryotes. Sda directly inhibits sporulation histidine kinases in response to DNA damage and replication defects. We determined a 2.0-A-resolution X-ray crystal structure of the intact cytoplasmic catalytic core [comprising the dimerization and histidine phosphotransfer domain (DHp domain), connected to the ATP binding catalytic domain] of the Geobacillus stearothermophilus sporulation kinase KinB complexed with Sda. Structural and biochemical analyses reveal that Sda binds to the base of the DHp domain and prevents molecular transactions with the DHp domain to which it is bound by acting as a simple molecular barricade. Sda acts to sterically block communication between the catalytic domain and the DHp domain, which is required for autophosphorylation, as well as to sterically block communication between the response regulator Spo0F and the DHp domain, which is required for phosphotransfer and phosphatase activities.


  • Organizational Affiliation
    • The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 60.89 kDa 
  • Atom Count: 4,224 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 534 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sporulation kinase B
A, B
244Geobacillus stearothermophilus 10Mutation(s): 0 
Gene Names: GK1832GKA09
EC: 2.7.13.3
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sporulation kinase inhibitor Sda46Geobacillus stearothermophilus 10Mutation(s): 0 
Gene Names: GK2527

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B],
J [auth B],
K [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.215 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.111α = 90
b = 66.111β = 90
c = 315.572γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations