1XHF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.jmb.2005.03.059
  • Primary Citation of Related Structures:  
    1XHE, 1XHF

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aerobic respiration control protein arcA
A, B
123Escherichia coliMutation(s): 6 
Gene Names: arcAdyefexAsfrAsegmspcpxC
UniProt
Find proteins for P0A9Q1 (Escherichia coli (strain K12))
Explore P0A9Q1 
Go to UniProtKB:  P0A9Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9Q1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BF4
Query on BF4

Download Ideal Coordinates CCD File 
H [auth B]BERYLLIUM TETRAFLUORIDE ION
Be F4
UUMYFIKVCFICLB-UHFFFAOYSA-J
BEF
Query on BEF

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
BF2
Query on BF2

Download Ideal Coordinates CCD File 
I [auth B]BERYLLIUM DIFLUORIDE
Be F2
JZKFIPKXQBZXMW-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.169α = 90
b = 86.169β = 90
c = 213.082γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations