5EPV

Histidine kinase domain from the LOV-HK blue-light receptor from Brucella abortus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain.

Rinaldi, J.Arrar, M.Sycz, G.Cerutti, M.L.Berguer, P.M.Paris, G.Estrin, D.A.Marti, M.A.Klinke, S.Goldbaum, F.A.

(2016) J Mol Biol 428: 1165-1179

  • DOI: 10.1016/j.jmb.2016.01.026
  • Primary Citation of Related Structures:  
    5EPV

  • PubMed Abstract: 
  • In response to light, as part of a two-component system, the Brucella blue light-activated histidine kinase (LOV-HK) increases its autophosphorylation, modulating the virulence of this microorganism. The Brucella histidine kinase (HK) domain belongs to the HWE family, for which there is no structural information ...

    In response to light, as part of a two-component system, the Brucella blue light-activated histidine kinase (LOV-HK) increases its autophosphorylation, modulating the virulence of this microorganism. The Brucella histidine kinase (HK) domain belongs to the HWE family, for which there is no structural information. The HWE family is exclusively present in proteobacteria and usually coupled to a wide diversity of light sensor domains. This work reports the crystal structure of the Brucella HK domain, which presents two different dimeric assemblies in the asymmetric unit: one similar to the already described canonical parallel homodimers (C) and the other, an antiparallel non-canonical (NC) dimer, each with distinct relative subdomain orientations and dimerization interfaces. Contrary to these crystallographic structures and unlike other HKs, in solution, the Brucella HK domain is monomeric and still active, showing an astonishing instability of the dimeric interface. Despite this instability, using cross-linking experiments, we show that the C dimer is the functionally relevant species. Mutational analysis demonstrates that the autophosphorylation activity occurs in cis. The different relative subdomain orientations observed for the NC and C states highlight the large conformational flexibility of the HK domain. Through the analysis of these alternative conformations by means of molecular dynamics simulations, we also propose a catalytic mechanism for Brucella LOV-HK.


    Related Citations: 
    • S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations.
      Klinke, S., Foos, N., Rinaldi, J.J., Paris, G., Goldbaum, F.A., Legrand, P., Guimaraes, B.G., Thompson, A.
      (2015) Acta Crystallogr D Biol Crystallogr 71: 1433

    Organizational Affiliation

    Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Avenida Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina. Electronic address: fgoldbaum@leloir.org.ar.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Blue-light-activated histidine kinaseA, B, C, D233Brucella abortus 2308Mutation(s): 0 
Gene Names: BAB2_0652
EC: 2.7.13.3
UniProt
Find proteins for Q2YKK7 (Brucella abortus (strain 2308))
Explore Q2YKK7 
Go to UniProtKB:  Q2YKK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YKK7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
J [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.39α = 90
b = 100.84β = 102.75
c = 71.41γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata scaling
PHASERphasing
SHELXphasing
MOLREPphasing
BUSTERrefinement
Cootmodel building
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Nacional de Promocion Cientifica y TecnologicaArgentinaPICT 2011-2672
National Scientific and Technical Research Council (CONICET)ArgentinaPIP 2012-2014 GI 220110100970

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence