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(-) Description

Title :  NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN/DNA COMPLEX
 
Authors :  J. M. Wojciak, J. Iwahara, R. T. Clubb
Date :  26 Oct 00  (Deposition) - 08 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (25x)
Keywords :  Protein/Dna Complex, Helix-Turn-Helix, Winged-Helix, Bacteriophage Mu, Repressor, Virus/Viral Protein, Viral Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Wojciak, J. Iwahara, R. T. Clubb
The Mu Repressor-Dna Complex Contains An Immobilized 'Wing' Within The Minor Groove.
Nat. Struct. Biol. V. 8 84 2001
PubMed-ID: 11135677  |  Reference-DOI: 10.1038/89582
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPRESSOR PROTEIN C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DNA-BINDING DOMAIN (RESIDUES 13-81)
    Gene: MU C
    Organism Scientific: ENTEROBACTERIA PHAGE MU
    Organism Taxid: 10677
    Synonym: MU BACTERIOPHAGE C REPRESSOR PROTEIN
 
Molecule 2 - 5'- D(P*CP*CP*TP*TP*TP*TP*CP*AP*GP*TP*AP*AP*TP*CP*TP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'- D(P*CP*AP*GP*AP*TP*TP*AP*CP*TP*GP*AP*AP*AP*AP*GP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (25x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1G4D)

(-) Sites  (0, 0)

(no "Site" information available for 1G4D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G4D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G4D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G4D)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MUPS51702 Mu-type HTH domain profile.REPC_BPMU13-81  1A:13-81

(-) Exons   (0, 0)

(no "Exon" information available for 1G4D)

(-) Sequences/Alignments

NMR Structure
   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:69
 aligned with REPC_BPMU | P06019 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:69
                                    22        32        42        52        62        72         
            REPC_BPMU    13 KSIWCSPQEIMAADGMPGSVAGVHYRANVQGWTKQKKEGVKGGKAVEYDVMSMPTKEREQVIAHLGLST  81
               SCOP domains d1g4da_ A: mu transposase, DNA-binding domain                         SCOP domains
               CATH domains 1g4dA00 A:13-81 'winged helix' repressor DNA binding domain           CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh......hhhhhhhhhhhhh..eee.........eee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_MU  PDB: A:13-81 UniProt: 13-81                                   PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1g4d A  13 KSIWCSPQEIMAADGMPGSVAGVHYRANVQGWTKRKKEGVKGGKAVEYDVMSMPTKEREQVIAHLGLST  81
                                    22        32        42        52        62        72         


Chain B from PDB  Type:DNA  Length:16
                                                
                 1g4d B 102 CCTTTTCAGTAATCTG 117
                                   111      


Chain C from PDB  Type:DNA  Length:16
                                                
                 1g4d C 120 CAGATTACTGAAAAGG 135
                                   129
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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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G4D)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (REPC_BPMU | P06019)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        REPC_BPMU | P06019: 1qpm

(-) Related Entries Specified in the PDB File

1qpm NMR STRUCTURE OF THE MU REPRESSOR DNA-BINDING DOMAIN IN THE ABSENCE OF DNA