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PDBsum entry 2cax
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protein dna_rna Protein-protein interface(s) links
Transcriptional repressor PDB id
2cax

 

 

 

 

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Contents
Protein chains
53 a.a.
50 a.a.
47 a.a.
DNA/RNA
Waters ×42
PDB id:
2cax
Name: Transcriptional repressor
Title: Structural basis for cooperative binding of ribbon-helix-helix repressor omega to mutated direct DNA heptad repeats
Structure: Orf omega. Chain: a, b, c, d. Fragment: ribbon-helix-helix domain, residues 20-71. Synonym: orf omega transcriptional repressor. Engineered: yes. Other_details: 19 n-terminal residues deleted, new n- terminal residue met19 is a cloning artefact. 5'-d( Gp Ap Ap Tp Cp Ap Cp Ap Ap Ap Tp Cp Ap Cp Ap Ap G)- 3'.
Source: Streptococcus pyogenes. Organism_taxid: 1314. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: omega transcriptional reprsssor is encoded by plasmid psm19035 of the inc18 family of plasmids.. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.
Biol. unit: Octamer (from PDB file)
Resolution:
2.90Å     R-factor:   0.210     R-free:   0.247
Authors: W.A.Weihofen,A.Cicek,F.Pratto,J.C.Alonso,W.Saenger
Key ref: W.A.Weihofen et al. (2006). Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription. Nucleic Acids Res, 34, 1450-1458. PubMed id: 16528102
Date:
23-Dec-05     Release date:   15-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57468  (Q57468_STRPY) -  Transcriptional repressor from Streptococcus pyogenes
Seq:
Struc: 		71 a.a.
53 a.a.*
Protein chain
Pfam   ArchSchema ?
Q57468  (Q57468_STRPY) -  Transcriptional repressor from Streptococcus pyogenes
Seq:
Struc: 		71 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
Q57468  (Q57468_STRPY) -  Transcriptional repressor from Streptococcus pyogenes
Seq:
Struc: 		71 a.a.
47 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-A-A-T-C-A-C-A-A-A-T-C-A-C-A-A-G 17 bases
  T-T-G-T-G-A-T-T-T-G-T-G-A-T-T-C-G 17 bases
  G-A-A-T-C-A-C-A-A-G-T-C-A-C-A-A-G-C 18 bases
  C-T-T-G-T-G-A-C-T-T-G-T-G-A-T-T-C-G 18 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Nucleic Acids Res 34:1450-1458 (2006)
PubMed id: 16528102  
 
 
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
W.A.Weihofen, A.Cicek, F.Pratto, J.C.Alonso, W.Saenger.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21123191 L.Huang, P.Yin, X.Zhu, Y.Zhang, and K.Ye (2011).
Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100.
  Nucleic Acids Res, 39, 2954-2968.
PDB code: 3no7
21217150 M.Komai, M.Umino, and R.Hanai (2011).
Mode of DNA binding by SopA protein of Escherichia coli F plasmid.
  J Biochem, 149, 455-461.  
21336656 N.Chopra, S.Agarwal, S.Verma, S.Bhatnagar, and R.Bhatnagar (2011).
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function.
  J Comput Aided Mol Des, 25, 275-291.  
21138966 N.E.Soberón, V.S.Lioy, F.Pratto, A.Volante, and J.C.Alonso (2011).
Molecular anatomy of the Streptococcus pyogenes pSM19035 partition and segrosome complexes.
  Nucleic Acids Res, 39, 2624-2637.  
20709902 E.A.Waligora, D.M.Ramsey, E.E.Pryor, H.Lu, T.Hollis, G.P.Sloan, R.Deora, and D.J.Wozniak (2010).
AmrZ beta-sheet residues are essential for DNA binding and transcriptional control of Pseudomonas aeruginosa virulence genes.
  J Bacteriol, 192, 5390-5401.  
20176965 M.P.Hui, V.E.Galkin, X.Yu, A.Z.Stasiak, A.Stasiak, M.K.Waldor, and E.H.Egelman (2010).
ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA.
  Proc Natl Acad Sci U S A, 107, 4590-4595.  
20639540 T.Massad, K.Skaar, H.Nilsson, P.Damberg, P.Henriksson-Peltola, E.Haggård-Ljungquist, M.Högbom, and P.Stenmark (2010).
Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats.
  Nucleic Acids Res, 38, 7778-7790.
PDB code: 2xcj
19726689 F.Pratto, Y.Suzuki, K.Takeyasu, and J.C.Alonso (2009).
Single-molecule analysis of proteinxDNA complexes formed during partition of newly replicated plasmid molecules in Streptococcus pyogenes.
  J Biol Chem, 284, 30298-30306.  
19759211 L.Ni, S.O.Jensen, N.Ky Tonthat, T.Berg, S.M.Kwong, F.H.Guan, M.H.Brown, R.A.Skurray, N.Firth, and M.A.Schumacher (2009).
The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes.
  Nucleic Acids Res, 37, 6970-6983.
PDB code: 3gxq
19376860 M.Zampini, A.Derome, S.E.Bailey, D.Barillà, and F.Hayes (2009).
Recruitment of the ParG segregation protein to different affinity DNA sites.
  J Bacteriol, 191, 3832-3841.  
18350140 A.J.Soler Bistué, D.Birshan, A.P.Tomaras, M.Dandekar, T.Tran, J.Newmark, D.Bui, N.Gupta, K.Hernandez, R.Sarno, A.Zorreguieta, L.A.Actis, and M.E.Tolmasky (2008).
Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements.
  PLoS ONE, 3, e1800.  
18477635 F.Pratto, A.Cicek, W.A.Weihofen, R.Lurz, W.Saenger, and J.C.Alonso (2008).
Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation.
  Nucleic Acids Res, 36, 3676-3689.
PDB code: 2oze
18586269 Y.Zhou, J.D.Larson, C.A.Bottoms, E.C.Arturo, M.T.Henzl, J.L.Jenkins, J.C.Nix, D.F.Becker, and J.J.Tanner (2008).
Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA.
  J Mol Biol, 381, 174-188.
PDB code: 2rbf
17676053 E.R.Schreiter, and C.L.Drennan (2007).
Ribbon-helix-helix transcription factors: variations on a theme.
  Nat Rev Microbiol, 5, 710-720.  
17898804 J.Møller-Jensen, S.Ringgaard, C.P.Mercogliano, K.Gerdes, and J.Löwe (2007).
Structural analysis of the ParR/parC plasmid partition complex.
  EMBO J, 26, 4413-4422.
PDB code: 2jd3
18097417 M.A.Schumacher, T.C.Glover, A.J.Brzoska, S.O.Jensen, T.D.Dunham, R.A.Skurray, and N.Firth (2007).
Segrosome structure revealed by a complex of ParR with centromere DNA.
  Nature, 450, 1268-1271.
PDB code: 2q2k
17656583 M.Oberer, K.Zangger, K.Gruber, and W.Keller (2007).
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.
  Protein Sci, 16, 1676-1688.
PDB code: 2an7
17905984 M.V.Francia, K.E.Weaver, P.Goicoechea, P.Tille, and D.B.Clewell (2007).
Characterization of an active partition system for the Enterococcus faecalis pheromone-responding plasmid pAD1.
  J Bacteriol, 189, 8546-8555.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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