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(-) Description

Title :  CRYSTAL STRUCTURE OF CVIR BOUND TO ANTAGONIST CHLOROLACTONE (CL)
 
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 :  3.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Quorum Sensing, Agonist, Antagonist, Luxr, Acylated Homoserine Lactone, Transcription Factor, Dna Binding Protein, Ligand Binding Domain, Signal Receptor, Quorum Sensing Transcription Factor, Chlorolactone (Cl), 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, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CVIR
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: 31532
    Synonym: TRANSCRIPTIONAL ACTIVATOR, LUXR/UHPA FAMILY OF REGULATORS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HLC4Ligand/Ion4-(4-CHLOROPHENOXY)-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]BUTANAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HLC2Ligand/Ion4-(4-CHLOROPHENOXY)-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]BUTANAMIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HLC2Ligand/Ion4-(4-CHLOROPHENOXY)-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]BUTANAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:57 , LEU A:72 , TYR A:80 , TRP A:84 , TYR A:88 , ASP A:97 , TRP A:111 , MET A:135 , SER A:155BINDING SITE FOR RESIDUE HLC A 266
2AC2SOFTWAREVAL A:250 , LEU B:57 , TYR B:80 , TRP B:84 , LEU B:85 , TYR B:88 , ASP B:97 , ILE B:99 , TRP B:111 , PHE B:115 , PHE B:126 , SER B:155BINDING SITE FOR RESIDUE HLC B 266
3AC3SOFTWARELEU C:57 , TYR C:80 , TRP C:84 , TYR C:88 , ASP C:97 , TRP C:111 , MET C:135 , SER C:155 , VAL D:250BINDING SITE FOR RESIDUE HLC C 266
4AC4SOFTWAREVAL C:250 , LEU D:57 , TYR D:80 , TRP D:84 , LEU D:85 , TYR D:88 , MET D:89 , ASP D:97 , ILE D:99 , TRP D:111 , MET D:135 , SER D:155BINDING SITE FOR RESIDUE HLC D 266

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QP5)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:107 -Pro A:108
2Pro A:190 -Ala A:191
3Pro A:193 -Ser A:194
4Leu A:198 -Ser A:199
5Gly B:15 -Leu B:16
6Asn B:187 -Leu B:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QP5)

(-) Exons   (0, 0)

(no "Exon" information available for 3QP5)

(-) 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:251
 aligned with D3W065_CHRVL | D3W065 from UniProtKB/TrEMBL  Length:265

    Alignment length:251
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258 
         D3W065_CHRVL     9 ARPLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMPP 259
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeee...hhhhhhhhhhh.................eehhhhhh...hhhhhhhhhhhh......eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qp5 A   9 ARPLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMPP 259
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258 


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with D3W065_CHRVL | D3W065 from UniProtKB/TrEMBL  Length:265

    Alignment length:245
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253     
         D3W065_CHRVL    14 AGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMP 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh....hhhhhhhhhhhhh.........eeeee.........eeee......hhhhhhhhhh.................eehhhhhh...hhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------..hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qp5 B  14 AGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLP-------PLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMP 258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     |   -   |   203       213       223       233       243       253     
                                                                                                                                                                                                         189     197                                                             


Chain C from PDB  Type:PROTEIN  Length:239
 aligned with D3W065_CHRVL | D3W065 from UniProtKB/TrEMBL  Length:265

    Alignment length:248
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
         D3W065_CHRVL    11 PLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMP 258
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee....hhhhhhhhhhh.................eehhhhhh...hhhhhhhhhhhh......eeeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.---------.hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qp5 C  11 PLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANL---------LSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHLAMP 258
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -       200       210       220       230       240       250        
                                                                                                                                                                                                           188       198                                                            


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with D3W065_CHRVL | D3W065 from UniProtKB/TrEMBL  Length:265

    Alignment length:246
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
         D3W065_CHRVL    10 RPLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANLPPASPSNMPLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHL 255
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......eeeeeeee.....eeeeeee.....hhhhhhhhhhh..................hhhhhhh...hhhhhhhhhhhh.......eeeeeeehhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...--------..hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qp5 D  10 RPLPAGLTASQQWTLLEWIHMAGHIETENELKAFLDQVLSQAPSERLLLALGRLNNQNQIQRLERVLNVSYPSDWLDQYMKENYAQHDPILRIHLGQGPVMWEERFNRAKGAEEKRFIAEATQNGMGSGITFSAASERNNIGSILSIAGREPGRNAALVAMLNCLTPHLHQAAIRVANL--------PLSQREYDIFHWMSRGKTNWEIATILDISERTVKFHVANVIRKLNANNRTHAIVLGMHL 255
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        |-       199       209       219       229       239       249      
                                                                                                                                                                                                            188      197
   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 3QP5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QP5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QP5)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (D3W065_CHRVL | D3W065)
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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  3qp5
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  D3W065_CHRVL | D3W065
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 Related Entries

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

UniProtKB/TrEMBL
        D3W065_CHRVL | D3W065: 3qp1 3qp2 3qp4

(-) 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
3qp6 CRYSTAL STRUCTURE OF CVIR (CHROMOBACTERIUM VIOLACEUM 12472) BOUND TO C6-HSL
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