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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  E. COLI TRP APOREPRESSOR
 
Authors :  B. Benoff, J. Carey, H. M. Berman, C. L. Lawson
Date :  08 Jul 11  (Deposition) - 20 Jul 11  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  N,R
Keywords :  Helix-Turn-Helix Motif, Dna Binding, Trp Operator, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Carey, B. Benoff, B. Harish, L. Yuan, C. L. Lawson
Environment-Dependent Long-Range Structural Distortion In A Temperature-Sensitive Point Mutant.
Protein Sci. V. 21 63 2012
PubMed-ID: 22057811  |  Reference-DOI: 10.1002/PRO.759

(-) Compounds

Molecule 1 - TRP OPERON REPRESSOR
    Chains: R, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B4393, JW4356, RTRY, TRPR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : NR

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3SSW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SSW)

(-) 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 N from PDB  Type:PROTEIN  Length:98
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:98
                                    17        27        37        47        57        67        77        87        97        
           TRPR_ECOLI     8 SAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d3sswn_ N: Trp repressor, TrpR                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3ssw N   8 SAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    17        27        37        47        57        67        77        87        97        


Chain R from PDB  Type:PROTEIN  Length:101
 aligned with TRPR_ECOLI | P0A881 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:101
                                    14        24        34        44        54        64        74        84        94       104 
           TRPR_ECOLI     5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
               SCOP domains d3sswr_ R: Trp repressor, TrpR                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3ssw R   5 SPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL 105
                                    14        24        34        44        54        64        74        84        94       104
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0 ; only for superseded entry 1P6Z: 1,2)

(no "CATH Domain" information available for 3SSW, only for superseded entry 1P6Z replaced by 3SSW)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain N,R   (TRPR_ECOLI | P0A881)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPR_ECOLI | P0A881: 1co0 1jhg 1mi7 1rcs 1tro 1trr 1wrp 1wrs 1wrt 1zt9 2oz9 3ssx 3wrp

(-) Related Entries Specified in the PDB File

3ssx E. COLI TRP APOREPORESSOR L75F MUTANT