Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 51.52 kDa 
• Atom Count: 3227 
• Residue Count: 385 
• Unique protein chains: 1

3EHH

Crystal structure of DesKC-H188V in complex with ADP

• DOI: 10.2210/pdb3EHH/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-09-12 Released: 2009-09-15 
• Deposition Author(s): Albanesi, D., Alzari, P.M., Buschiazzo, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structural plasticity and catalysis regulation of a thermosensor histidine kinase

Albanesi, D., Martin, M., Trajtenberg, F., Mansilla, M.C., Haouz, A., Alzari, P.M., de Mendoza, D., Buschiazzo, A.

(2009) Proc Natl Acad Sci U S A 106: 16185-16190

• PubMed: 19805278 
• DOI: 10.1073/pnas.0906699106
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Temperature sensing is essential for the survival of living cells. A major challenge is to understand how a biological thermometer processes thermal information to optimize cellular functions. Using structural and biochemical approaches, we show that the thermosensitive histidine kinase, DesK, from Bacillus subtilis is cold-activated through specific interhelical rearrangements in its central four-helix bundle domain. As revealed by the crystal structures of DesK in different functional states, the plasticity of this helical domain influences the catalytic activities of the protein, either by modifying the mobility of the ATP-binding domains for autokinase activity or by modulating binding of the cognate response regulator to sustain the phosphotransferase and phosphatase activities. The structural and biochemical data suggest a model in which the transmembrane sensor domain of DesK promotes these structural changes through conformational signals transmitted by the membrane-connecting two-helical coiled-coil, ultimately controlling the alternation between output autokinase and phosphatase activities. The structural comparison of the different DesK variants indicates that incoming signals can take the form of helix rotations and asymmetric helical bends similar to those reported for other sensing systems, suggesting that a similar switching mechanism could be operational in a wide range of sensor histidine kinases.

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Organizational Affiliation: 

Institut Pasteur, Unité de Biochimie Structurale and Plateforme de Cristallogenèse et Diffraction de Rayons X, URA 2185 Centre National de la Recherche Scientifique, Paris 75015, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sensor kinase (YocF protein)	A, B	218	Bacillus subtilis	Mutation(s): 3  Gene Names: yocF EC: 2.7.13.3
Find proteins for O34757 (Bacillus subtilis (strain 168)) Go to UniProtKB:  O34757

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.232 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.743	α = 90
b = 124.05	β = 90
c = 138.303	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-12 
• Released Date: 2009-09-15 
Deposition Author(s): Albanesi, D., Alzari, P.M., Buschiazzo, A.

Revision History 

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance