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(-) Description

Title :  C-TERMINAL DNA BINDING DOMAIN OF TRANSCRIPTIONAL PLEIOTROPIC REPRESSOR CODY.
 
Authors :  V. M. Levdikov, E. Blagova, P. Joseph, A. L. Sonenshein, A. J. Wilkinson
Date :  14 Sep 05  (Deposition) - 21 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C  (4x)
Keywords :  Cody, Dna-Binding; Nucleotide-Binding; Repressor; Transcription Regulation; Winged Hth Motif. , Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Levdikov, E. Blagova, P. Joseph, A. L. Sonenshein, A. J. Wilkinso
The Structure Of Cody, A Gtp- And Isoleucine-Responsive Regulator Of Stationary Phase And Virulence In Gram-Positiv Bacteria.
J. Biol. Chem. V. 281 11366 2006
PubMed-ID: 16488888  |  Reference-DOI: 10.1074/JBC.M513015200

(-) Compounds

Molecule 1 - GTP-SENSING TRANSCRIPTIONAL PLEIOTROPIC REPRESSOR CODY
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: CODY
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: VEGETATIVE PROTEIN 286B, VEG286B

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): AB 
Biological Unit 2 (4x):   C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B0L)

(-) Sites  (0, 0)

(no "Site" information available for 2B0L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B0L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B0L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B0L)

(-) Exons   (0, 0)

(no "Exon" information available for 2B0L)

(-) Sequences/Alignments

Asymmetric 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:98
 aligned with CODY_BACSU | P39779 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:98
                                   170       180       190       200       210       220       230       240       250        
           CODY_BACSU   161 EIEEEARSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENLKS 258
               SCOP domains ------d2b0la1 A:167-257 GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhhhh......eeeehhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.....eeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2b0l A 161 HHHHHHMSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENLKS 258
                                   170       180       190       200       210       220       230       240       250        


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with CODY_BACSU | P39779 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:95
                                   172       182       192       202       212       222       232       242       252     
           CODY_BACSU   163 EEEARSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENLK 257
               SCOP domains d2b0lb_ B: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhh......eeeehhhhhhhhhh.hhhhhhhhhhhhhhh..ee........eeeee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2b0l B 163 HHHHMSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENLK 257
                                   172       182       192       202       212       222       232       242       252     


Chain C from PDB  Type:PROTEIN  Length:94
 aligned with CODY_BACSU | P39779 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:94
                                   172       182       192       202       212       222       232       242       252    
           CODY_BACSU   163 EEEARSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENL 256
               SCOP domains d2b0lc_ C: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..hhhhhhhhhh......eeee...........hhhhhhhhhhhhhhh..eeee......eeeee..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2b0l C 163 HHHHMSKAVVQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELENL 256
                                   172       182       192       202       212       222       232       242       252
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B0L)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CODY_BACSU | P39779)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CODY_BACSU | P39779: 2b18 2gx5 2hgv 5lnh 5loe 5loj 5loo

(-) Related Entries Specified in the PDB File

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