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(-) Description

Title :  CRYSTAL STRUCTURE OF CVIR (CHROMOBACTERIUM VIOLACEUM 12472) BOUND TO C6-HSL
 
Authors :  G. Chen, L. Swem, D. Swem, D. Stauff, C. O'Loughlin, P. Jeffrey, B. Bassl F. Hughson
Date :  11 Feb 11  (Deposition) - 30 Mar 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Quorum Sensing, Agonist, Antagonist, Luxr, Acylated Homoserine Lactone, Transcription Factor, Dna Binding Protein, Ligand Binding Domain, Signal Receptor, N-Hexanoyl-L-Homoserine Lactone, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Chen, L. R. Swem, D. L. Swem, D. L. Stauff, C. T. O'Loughlin, P. D. Jeffrey, B. L. Bassler, F. M. Hughson
A Strategy For Antagonizing Quorum Sensing.
Mol. Cell V. 42 199 2011
PubMed-ID: 21504831  |  Reference-DOI: 10.1016/J.MOLCEL.2011.04.003

(-) Compounds

Molecule 1 - CVIR TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CVIR
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: 12472
    Synonym: TRANSCRIPTIONAL ACTIVATOR, LUXR/UHPA FAMILY OF REGULATORS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HL61Ligand/IonN-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HL62Ligand/IonN-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]HEXANAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:80 , TRP A:84 , ASP A:97 , ILE A:99 , TRP A:111 , PHE A:126 , MET A:135 , ILE A:153 , SER A:155BINDING SITE FOR RESIDUE HL6 A 266

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QP6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:50 -Ala A:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QP6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QP6)

(-) Exons   (0, 0)

(no "Exon" information available for 3QP6)

(-) 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:258
 aligned with Q7NQP7_CHRVO | Q7NQP7 from UniProtKB/TrEMBL  Length:265

    Alignment length:258
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256        
         Q7NQP7_CHRVO     7 INARPLPAGLTASQQWTLLEWIHMAGHIETEGELKAFLDNILSQAPSDRIILVLGRLNNQNQIQRMEKVLNVSYPSDWLNQYSQENFAQHDPIMRIHLGQGPVIWEERFSRAKGSEEKRFIAEASSNGMGSGITFSAASDRNNVGSILSIGGKEPGRNAALVAMLNCLTPHLHQAAVRIANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILNISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMTPRELVN 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------Autoind_bind-3qp6A01 A:36-182                                                                                                                      ------------GerE-3qp6A02 A:195-251                                   ------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eeeeeeeee.....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh......eehhhhhh...hhhhhhhhhhhhhh....eeeeeee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qp6 A   7 INARPLPAGLTASQQWTLLEWIHMAGHIETEGELKAFLDNILSQAPSDRIILVLGRLNNQNQIQRMEKVLNVSYPSDWLNQYSQENFAQHDPIMRIHLGQGPVIWEERFSRAKGSEEKRFIAEASSNGMGSGITFSAASDRNNVGSILSIGGKEPGRNAALVAMLNCLTPHLHQAAVRIANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILNISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMTPRELVN 264
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3QP6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QP6)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GAF (44)
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7NQP7_CHRVO | Q7NQP7)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q7NQP7_CHRVO | Q7NQP7: 3qp8

(-) Related Entries Specified in the PDB File

3qp1 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C6-HSL
3qp2 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C8-HSL
3qp4 CRYSTAL STRUCTURE OF CVIR LIGAND-BINDING DOMAIN BOUND TO C10-HSL
3qp5 CRYSTAL STRUCTURE OF CVIR BOUND TO ANTAGONIST CHLOROLACTONE (CL)
3qp7 CRYSTAL STRUCTURE OF SEMET CVIR (CHROMOBACTERIUM VIOLACEUM 12472) BOUND TO C6-HSL
3qp8 CRYSTAL STRUCTURE OF CVIR (CHROMOBACTERIUM VIOLACEUM 12472) BOUND TO C10-HSL