2BNW

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

• PDB DOI:  https://doi.org/10.2210/pdb2BNW/pdb
• NAKB: 2BNW

• Classification: DNA-BINDING/REGULATORY PROTEIN
• Organism(s): Streptococcus pyogenes, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-04-05 Released: 2006-03-15 
• Deposition Author(s): Weihofen, W.A., Cicek, A., Pratto, F., Alonso, J.C., Saenger, W.

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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 

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

• PubMed: 16528102 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 46.61 kDa 
• Atom Count: 3,153 
• Modelled Residue Count: 274 
• Deposited Residue Count: 284 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF OMEGA	A, B, C, D	53	Streptococcus pyogenes	Mutation(s): 0  Gene Names: omega
UniProt
Find proteins for Q57468 (Streptococcus pyogenes) Explore Q57468  Go to UniProtKB:  Q57468

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'	E, G	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'	F, H	18	synthetic construct

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 = 219.426	α = 90
b = 44.631	β = 108.8
c = 75.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-15 
Deposition Author(s): Weihofen, W.A., Cicek, A., Pratto, F., Alonso, J.C., Saenger, W.

Revision History  

• 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