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(-) Description

Title :  STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO DIRECT DNA HEPTAD REPEATS
 
Authors :  W. A. Weihofen, A. Cicek, F. Pratto, J. C. Alonso, W. Saenger
Date :  05 Apr 05  (Deposition) - 15 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Dna-Binding-Regulatory Protein Complex, Ribbon-Helix-Helix, Rhh, Metj/Arc Superfamily, Cooperative Dna Binding, Inverted Repeats, Dna Heptad, Inc18 Family, Dna-Binding Regulatory Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. A. Weihofen, A. Cicek, F. Pratto, J. C. Alonso, W. Saenger
Structures Of Omega Repressors Bound To Direct And Inverted Dna Repeats Explain Modulation Of Transcription.
Nucleic Acids Res. V. 34 1450 2006
PubMed-ID: 16528102  |  Reference-DOI: 10.1093/NAR/GKL015

(-) Compounds

Molecule 1 - ORF OMEGA
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-DELTA19OMEGA
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71
    Organism CommonSTREPTOCOCCUS
    Organism ScientificSTREPTOCOCCUS PYOGENES
    Organism Taxid1314
    Other DetailsOMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS
    SynonymOMEGA TRANSCRIPTIONAL REPRESSOR, ORF OMEGA'
 
Molecule 2 - 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'
    ChainsE, G
    Other DetailsSEQUENCE: 5'- GAA TCA CAA ATC ACA AGC -3', 18MER DNA OLIGONUCLEOTIDE, FIRST STRAND, DIRECT DNA HEPTAD REPEATS (5'- AATCACA -3')
    Other Details - SourceDIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
    ChainsF, H
    Other DetailsSEQUENCE: 5'- CTT GTG ATT TGT GAT TCG -3', 18MER DNA OLIGONUCLEOTIDE, SECOND STRAND
    Other Details - SourceDIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BNW)

(-) Sites  (0, 0)

(no "Site" information available for 2BNW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BNW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BNW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BNW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BNW)

(-) Exons   (0, 0)

(no "Exon" information available for 2BNW)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:49
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:49
                                    32        42        52        62         
          Q57468_STRPY   23 DIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnwa_ A: automated matches                      SCOP domains
               CATH domains 2bnwA00 A:23-71 Met repressor-like                CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                  2bnw A 23 DIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    32        42        52        62         

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:53
                                    28        38        48        58        68   
          Q57468_STRPY   19 SAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnwb_ B: automated matches                          SCOP domains
               CATH domains 2bnwB00 B:19-71 Met repressor-like                    CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bnw B 19 MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    28        38        48        58        68   

Chain C from PDB  Type:PROTEIN  Length:53
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:53
                                    28        38        48        58        68   
          Q57468_STRPY   19 SAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnwc_ C: automated matches                          SCOP domains
               CATH domains 2bnwC00 C:19-71 Met repressor-like                    CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eeeeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2bnw C 19 MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    28        38        48        58        68   

Chain D from PDB  Type:PROTEIN  Length:47
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:47
                                    34        44        54        64       
          Q57468_STRPY   25 MGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnwd_ D: automated matches                    SCOP domains
               CATH domains 2bnwD00 D:25-71 Met repressor-like              CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2bnw D 25 MGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    34        44        54        64       

Chain E from PDB  Type:DNA  Length:18
                                                 
                  2bnw E  1 GAATCACAAATCACAAGC 18
                                    10        

Chain F from PDB  Type:DNA  Length:18
                                                 
                  2bnw F 19 CTTGTGATTTGTGATTCG 36
                                    28        

Chain G from PDB  Type:DNA  Length:18
                                                 
                  2bnw G  1 GAATCACAAATCACAAGC 18
                                    10        

Chain H from PDB  Type:DNA  Length:18
                                                 
                  2bnw H 19 CTTGTGATTTGTGATTCG 36
                                    28        

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BNW)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q57468_STRPY | Q57468)
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q57468_STRPY | Q574681irq 2bnz 2cax

(-) Related Entries Specified in the PDB File

1irq CRYSTAL STRUCTURE OF OMEGA TRANSCRIPTIONAL REPRESSOR AT1.5A RESOLUTION
2bnz STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO INVERTED DNA HEPTAD REPEATS
2cax STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS