1XHF

Crystal structure of the bef3-activated receiver domain of redox response regulator arca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.152 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the alpha4-beta5-alpha5 Face

Toro-Roman, A.Mack, T.R.Stock, A.M.

(2005) J.Mol.Biol. 349: 11-26

  • DOI: 10.1016/j.jmb.2005.03.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli react to changes from aerobic to anaerobic conditions of growth using the ArcA-ArcB two-component signal transduction system. This system, in conjunction with other proteins, regulates the respiratory metabolic pathways in the organi ...

    Escherichia coli react to changes from aerobic to anaerobic conditions of growth using the ArcA-ArcB two-component signal transduction system. This system, in conjunction with other proteins, regulates the respiratory metabolic pathways in the organism. ArcA is a member of the OmpR/PhoB subfamily of response regulator transcription factors that are known to regulate transcription by binding in tandem to target DNA direct repeats. It is still unclear in this subfamily how activation by phosphorylation of the regulatory domain of response regulators stimulates DNA binding by the effector domain and how dimerization and domain orientation, as well as intra- and intermolecular interactions, affect this process. In order to address these questions we have solved the crystal structures of the regulatory domain of ArcA in the presence and absence of the phosphoryl analog, BeF3-. In the crystal structures, the regulatory domain of ArcA forms a symmetric dimer mediated by the alpha4-beta5-alpha5 face of the protein and involving a number of residues that are highly conserved in the OmpR/PhoB subfamily. It is hypothesized that members of this subfamily use a common mechanism of regulation by dimerization. Additional biophysical studies were employed to probe the oligomerization state of ArcA, as well as its individual domains, in solution. The solution studies show the propensity of the individual domains to associate into oligomers larger than the dimer observed for the intact protein, and suggest that the C-terminal DNA-binding domain also plays a role in oligomerization.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aerobic respiration control protein arcA
A, B
123Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: arcA (cpxC, dye, fexA, msp, seg, sfrA)
Find proteins for P0A9Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9Q1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BF2
Query on BF2

Download SDF File 
Download CCD File 
B
BERYLLIUM DIFLUORIDE
Be F2
JZKFIPKXQBZXMW-UHFFFAOYSA-L
 Ligand Interaction
BF4
Query on BF4

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Download CCD File 
B
BERYLLIUM TETRAFLUORIDE ION
Be F4
UUMYFIKVCFICLB-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.152 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.169α = 90.00
b = 86.169β = 90.00
c = 213.082γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance