2CAX

STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription.

Weihofen, W.A.Cicek, A.Pratto, F.Alonso, J.C.Saenger, W.

(2006) Nucleic Acids Res. 34: 1450

  • DOI: 10.1093/nar/gkl015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Repressor omega regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. omega belongs to homodimeric ribbon-helix-helix (RHH2) repressors typif ...

    Repressor omega regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. omega belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel beta-sheet for DNA major groove binding. Homodimeric omega2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5'-(A)/(T)ATCAC(A)/(T)-3', symbolized by -->) in palindromic inverted, converging (--><--) or diverging (<---->) orientation and also, unique to omega2 and contrasting other RHH2 repressors, to non-palindromic direct (-->-->) repeats. Here we investigate with crystal structures how omega2 binds specifically to heptads in minimal operators with (-->-->) and (--><--) repeats. Since the pseudo-2-fold axis relating the monomers in omega(2) passes the central C-G base pair of each heptad with approximately 0.3 A downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (-->-->), approximately 0.6 A shorter in (--><--) but would be approximately 0.6 A longer in (<---->). These variations grade interactions between adjacent omega2 and explain modulations in cooperative binding affinity of omega2 to operators with different heptad orientations.


    Organizational Affiliation

    Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF OMEGA
A, B, C, D
53Streptococcus pyogenesMutation(s): 0 
Gene Names: omega
Find proteins for Q57468 (Streptococcus pyogenes)
Go to UniProtKB:  Q57468
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3'G17N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3'H17N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3'U18N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'Y18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 219.957α = 90.00
b = 44.655β = 109.26
c = 76.136γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance