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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO INVERTED DNA HEPTAD REPEATS
 
Authors :  W. A. Weihofen, A. Cicek, F. Pratto, J. C. Alonso, W. Saenger
Date :  06 Apr 05  (Deposition) - 15 Mar 06  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Dna Binding Protein-Dna Complex, Ribbon-Helix-Helix, Rhh, Metj/Arc Superfamily, Cooperative Dna Binding, Inc18 Family (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
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-DELTA19OMEGA
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Other Details: OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS
    Synonym: OMEGA TRANSCRIPTIONAL REPRESSOR, ORF OMEGA'
 
Molecule 2 - 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'
    Chains: E, G
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SEQUENCE: 5'- GAA TCA CAA GTG ATT AGC -3', 18MER DNA OLIGONUCLEOTIDE, FIRST STRAND, INVERTED DNA HEPTAD REPEATS (5'- AATCAC A/T -3'), NUCLEOTIDES G5 - G16, G18 AND E18 WERE NOT MODELLED
    Other Details - Source: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
    Chains: F, H
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SEQUENCE: 5'- CTA ATC ACT TGT GAT TCG -3', 18MER DNA OLIGONUCLEOTIDE, SECOND STRAND, NUCLEOTIDES H19 - H31 WERE NOT MODELLED
    Other Details - Source: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
    Synthetic: YES

 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 2BNZ)

(-) Sites  (0, 0)

(no "Site" information available for 2BNZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BNZ)

(-) 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:50
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:50
                                    31        41        51        61        71
          Q57468_STRPY   22 KDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnza_ A: automated matches                       SCOP domains
               CATH domains 2bnzA00 A:22-71 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
                  2bnz A 22 KDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    31        41        51        61        71


Chain B from PDB  Type:PROTEIN  Length:50
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:50
                                    31        41        51        61        71
          Q57468_STRPY   22 KDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnzb_ B: automated matches                       SCOP domains
               CATH domains 2bnzB00 B:22-71 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
                  2bnz B 22 KDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    31        41        51        61        71


Chain C from PDB  Type:PROTEIN  Length:52
 aligned with Q57468_STRPY | Q57468 from UniProtKB/TrEMBL  Length:71

    Alignment length:52
                                    29        39        49        59        69  
          Q57468_STRPY   20 AKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
               SCOP domains d2bnzc_ C: automated matches                         SCOP domains
               CATH domains 2bnzC00 C:20-71 Met repressor-like                   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  2bnz C 20 AKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    29        39        49        59        69  


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 d2bnzd_ D: automated matches                    SCOP domains
               CATH domains 2bnzD00 D:25-71 Met repressor-like              CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2bnz D 25 MGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    34        44        54        64       


Chain E from PDB  Type:DNA  Length:17
                                                
                  2bnz E  1 GAATCACAAGTGATTAG 17
                                    10       


Chain F from PDB  Type:DNA  Length:18
                                                 
                  2bnz F 19 CTAATCACTTGTGATTCG 36
                                    28        


Chain G from PDB  Type:DNA  Length:5
                                    
                  2bnz G  1 GAATG 17
                               ||
                               4|
                               17


Chain H from PDB  Type:DNA  Length:5
                                    
                  2bnz H 32 ATTCG 36
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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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) 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 | Q57468: 1irq 2bnw 2cax

(-) Related Entries Specified in the PDB File

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