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(-) Description

Title :  CPRK OCPA DNA COMPLEX
 
Authors :  C. Levy
Date :  15 Aug 08  (Deposition) - 30 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Cprk, Halorespiration, Transcriptional Regulator, Transcription Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Levy, K. Pike, D. J. Heyes, M. G. Joyce, K. Gabor, H. Smidt, J. Van Der Oost, D. Leys
Molecular Basis Of Halorespiration Control By Cprk, A Crp-Fnr Type Transcriptional Regulator
Mol. Microbiol. V. 70 151 2008
PubMed-ID: 18717788  |  Reference-DOI: 10.1111/J.1365-2958.2008.06399.X

(-) Compounds

Molecule 1 - CYCLIC NUCLEOTIDE-BINDING PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHAF_0678
    Mutation: YES
    Organism Scientific: DESULFITOBACTERIUM HAFNIENSE
    Organism Taxid: 272564
    Strain: DCB-2
    Synonym: CPRK
 
Molecule 2 - DNA (5'- D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
13C41Ligand/Ion(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13C42Ligand/Ion(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR C:76 , ILE C:84 , GLY C:85 , LYS C:86 , THR C:90 , ASN C:92 , ILE C:94 , TYR C:130 , LEU C:131 , LYS C:133BINDING SITE FOR RESIDUE 3C4 C 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E6C)

(-) Exons   (0, 0)

(no "Exon" information available for 3E6C)

(-) 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:DNA  Length:13
                                             
                 3e6c A 534 GGCATGTTAATGC 546
                                   543   


Chain B from PDB  Type:DNA  Length:13
                                             
                 3e6c B 501 GCATTAACATGCC 513
                                   510   


Chain C from PDB  Type:PROTEIN  Length:225
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:225
                                                                                                                                                                                                                                                         232 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   | 
         B8FW11_DESHD     9 DFCGAIIPDNFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLSEQTSYY-   -
               SCOP domains d3e6cc2 C:9-147 Chlorophenol reduction protein CprK                                                                                        d3e6cc1 C:148-233 Chlorophenol reduction protein CprK                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhheeeee....eee........eeeeee..eeeeee.....eeeeeee....ee.........eeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhheee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee...eeee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6c C   9 DFCGAIIPDNFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDKKKNKIIVYNLGELKHLSEQTSYYS 233
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E6C)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain C   (B8FW11_DESHD | B8FW11)
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.

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  3e6c
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 Related Entries

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

UniProtKB/TrEMBL
        B8FW11_DESHD | B8FW11: 3e5q 3e5u 3e5x 3e6b 3e6d

(-) Related Entries Specified in the PDB File

3e5q 3e5u 3e6b 3e6d 3e6x