Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60894.80 
• Atom Count: 3851 
• Residue Count: 534 
• Unique protein chains: 2

3D36

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

• DOI: 10.2210/pdb3D36/pdb

• Classification: Transferase/Transferase inhibitor
• Expression System: Escherichia coli


• Deposited: 2008-05-09 Released: 2009-01-13 
• Deposition Author(s): Bick, M.J., Lamour, V., Rajashankar, K.R., Gordiyenko, Y., Robinson, C.V., Darst, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.215 
• R-Value Work: 0.200 

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.Biol. 386: 163-177

• PubMed: 19101565 
• DOI: 10.1016/j.jmb.2008.12.006


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sporulation kinase B	A, B	244	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Sporulation kinase inhibitor Sda	C	46	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
MPD	B, C	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.215 
• R-Value Work: 0.200 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 66.111	α = 90.00
b = 66.111	β = 90.00
c = 315.572	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data collection
HKL-2000	data reduction
PDB_EXTRACT	data extraction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-09 
• Released Date: 2009-01-13 
• Deposition Author(s): Bick, M.J., Lamour, V., Rajashankar, K.R., Gordiyenko, Y., Robinson, C.V., Darst, S.A.

Revision History 

• Version 1.0: 2009-01-13
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance