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(-) Description

Title :  RECOGNITION OF AT-RICH DNA BINDING SITES BY THE MOGR REPRESSOR
 
Authors :  A. Shen, D. E. Higgins, D. Panne
Date :  26 Nov 08  (Deposition) - 02 Jun 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Helix-Turn-Helix, Minor Groove Binding, Cytoplasm, Dna-Binding, Repressor, Transcription, Transcription Regulation, Virulence, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shen, D. E. Higgins, D. Panne
Recognition Of At-Rich Dna Binding Sites By The Mogr Repressor.
Structure V. 17 769 2009
PubMed-ID: 19446532  |  Reference-DOI: 10.1016/J.STR.2009.02.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MOTILITY GENE REPRESSOR MOGR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: LMO0674, MOGR
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
 
Molecule 2 - 5'- D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3'
    Chains: C
    Engineered: YES
    Other Details: FLAA PROMOTER SEQUENCE
    Synthetic: YES
 
Molecule 3 - 5'- D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3'
    Chains: D
    Engineered: YES
    Other Details: FLAA PROMOTER SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3FDQ)

(-) Sites  (0, 0)

(no "Site" information available for 3FDQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FDQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FDQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FDQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FDQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3FDQ)

(-) 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:140
 aligned with MOGR_LISM4 | G2K449 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           MOGR_LISM4     4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdq A   4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143


Chain A from PDB  Type:PROTEIN  Length:140
 aligned with MOGR_LISMO | P0DJO8 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           MOGR_LISMO     4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdq A   4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with MOGR_LISM4 | G2K449 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           MOGR_LISM4     4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdq B   4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with MOGR_LISMO | P0DJO8 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           MOGR_LISMO     4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdq B   4 SEIRKLLQEIKKQVDNPGNSSTTEIKKMASEAGIDEQTAEEIYHLLTEFYQAVEEHGGIEKYMHSNISWLKIELELLSACYQIAILEDMKVLDISEMLSLNDLRIFPKTPSQLQNTYYKLKKELIQVEDIPKNKPGRKRK 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143


Chain C from PDB  Type:DNA  Length:15
                                               
                 3fdq C   1 ATTTTTTAAAAAAAT  15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                               
                 3fdq D   1 TATTTTTTTAAAAAA  15
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 3FDQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FDQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FDQ)

(-) Gene Ontology  (5, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MOGR_LISMO | P0DJO8)
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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (MOGR_LISM4 | G2K449)
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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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