2BNW

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    2BNW, 2BNZ, 2CAX

  • 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 typified by a central, antiparallel beta-sheet for DNA major groove binding ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF OMEGAA, B, C, D53Streptococcus pyogenesMutation(s): 0 
Gene Names: omega
UniProt
Find proteins for Q57468 (Streptococcus pyogenes)
Explore Q57468 
Go to UniProtKB:  Q57468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57468
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'E, G 18synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'F, H 18synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.426α = 90
b = 44.631β = 108.8
c = 75.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Changes: Other, Source and taxonomy