3GIG

Crystal structure of phosphorylated DesKC in complex with AMP-PCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1073/pnas.0906699106
  • Primary Citation of Related Structures:  
    3EHF, 3EHH, 3EHJ, 3GIE, 3GIF, 3GIG

  • 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 ...

    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.


    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sensor histidine kinase desKA218Bacillus subtilisMutation(s): 0 
Gene Names: yocF
EC: 2.7.13.3
Find proteins for O34757 (Bacillus subtilis (strain 168))
Explore O34757 
Go to UniProtKB:  O34757
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sensor histidine kinase desKB218Bacillus subtilisMutation(s): 0 
Gene Names: yocF
EC: 2.7.13.3
Find proteins for O34757 (Bacillus subtilis (strain 168))
Explore O34757 
Go to UniProtKB:  O34757
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download CCD File 
A, B
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
BL-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.291 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.63α = 90
b = 94.63β = 90
c = 162.46γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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