1R71

Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB.

Khare, D.Ziegelin, G.Lanka, E.Heinemann, U.

(2004) Nat.Struct.Mol.Biol. 11: 656-663

  • DOI: 10.1038/nsmb773

  • PubMed Abstract: 
  • The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the p ...

    The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the plasmid's partitioning system. The protein structure consists of eight helices, two of which belong to a predicted helix-turn-helix motif. Each half-site of the palindromic operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based mainly on two side chain interactions outside the helix-turn-helix motif with two bases next to the central base pair of the 13-base pair operator sequence. The surface of the KorB DNA-binding domain mirrors the overall acidity of KorB, whereas DNA binding occurs via a basic interaction surface. We present a model of KorB, including the structure of its dimerization domain, and discuss its interactions with the highly basic ParA homolog IncC.


    Organizational Affiliation

    Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcriptional repressor protein korB
A, B, C, D
178Escherichia coliMutation(s): 0 
Gene Names: korB
Find proteins for P07674 (Escherichia coli)
Go to UniProtKB:  P07674
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'E,J,G,K17N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'I,F,L,H17N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
E, F, G, H, I, J, K, L
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.440α = 90.00
b = 110.440β = 90.00
c = 160.530γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata scaling
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description