Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS
 
Authors :  W. A. Weihofen, A. Cicek, F. Pratto, J. C. Alonso, W. Saenger
Date :  23 Dec 05  (Deposition) - 15 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,G,H,U,Y
Keywords :  Transcriptional Repressor, Inc18 Family Of Plasmids, Rhh, Metj/Arc Superfamily, Cooperative Dna Binding, Dna Heptad 5'- A/T Atcac A/T -3', Plasmid Maintenance, 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
    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: 19 N-TERMINAL RESIDUES DELETED, NEW N- TERMINAL RESIDUE MET19 IS A CLONING ARTEFACT
    Other Details - Source: OMEGA TRANSCRIPTIONAL REPRSSSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS.
    Synonym: ORF OMEGA TRANSCRIPTIONAL REPRESSOR
 
Molecule 2 - 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3'
    Chains: U
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
    Chains: Y
    Other Details: 18 BASE-PAIRS WITH G, C OVERHANGS. COGNATE HEPTAD D(AATCACA) FOLLOWED BY MUTATED HEPTAD D(AGTCACA)
    Other Details - Source: IN INC18 FAMILY PLASMIDS, DIRECT REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR
    Synthetic: YES
 
Molecule 4 - 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3'
    Chains: G
    Synthetic: YES
 
Molecule 5 - 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3'
    Chains: H
    Other Details: 17 BASE-PAIRS AND G, C OVERHANGS, COMPLEMENTARY STRAND TO FIRST STRAND
    Other Details - Source: IN INC18 FAMILY PLASMIDS, DIRECT REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDGHUY

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2CAX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CAX)

(-) 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: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 d2caxa_ A: automated matches                          SCOP domains
               CATH domains 2caxA00 A: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
                  2cax A 19 MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    28        38        48        58        68   


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 d2caxb_ B: automated matches                       SCOP domains
               CATH domains 2caxB00 B:22-71 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
                  2cax B 22 KDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    31        41        51        61        71


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 d2caxc_ C: automated matches                          SCOP domains
               CATH domains 2caxC00 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
                  2cax 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 d2caxd_ D: automated matches                    SCOP domains
               CATH domains 2caxD00 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
                  2cax D 25 MGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL 71
                                    34        44        54        64       


Chain G from PDB  Type:DNA  Length:17
                                                
                  2cax G  2 GAATCACAAATCACAAG 18
                                    11       


Chain H from PDB  Type:DNA  Length:17
                                                
                  2cax H 22 TTGTGATTTGTGATTCG 38
                                    31       


Chain U from PDB  Type:DNA  Length:18
                                                 
                  2cax U  1 GAATCACAAGTCACAAGC 18
                                    10        


Chain Y from PDB  Type:DNA  Length:18
                                                 
                  2cax Y 21 CTTGTGACTTGTGATTCG 38
                                    30
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 2CAX)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2cax)
 
  Sites
(no "Sites" information available for 2cax)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cax)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2cax
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q57468_STRPY | Q57468
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q57468_STRPY | Q57468
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q57468_STRPY | Q57468: 1irq 2bnw 2bnz

(-) 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
2bnz STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO INVERTED DNA HEPTAD REPEATS