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(-) Description

Title :  CRYSTAL STRUCTURE OF TTGV IN COMPLEX WITH ITS DNA OPERATOR
 
Authors :  D. Lu, S. Fillet, C. Meng, Y. Alguel, P. Kloppsteck, J. Bergeron, T. Krel M. -T. Gallegos, J. Ramos, X. Zhang
Date :  17 Sep 10  (Deposition) - 01 Dec 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B,E,F,X,Y
Keywords :  Dna-Binding Protein-Dna Complex, Tetrameric Gene Regulator, Cooperative Dna Binding, Multidrug Binding Protein, Antibiotic Resistance, Complex ( Dna-Binding Protein/Dna ) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Lu, S. Fillet, C. Meng, Y. Alguel, P. Kloppsteck, J. Bergeron, T. Krell, M. T. Gallegos, J. Ramos, X. Zhang
Crystal Structure Of Ttgv In Complex With Its Dna Operator Reveals A General Model For Cooperative Dna Binding Of Tetrameric Gene Regulators.
Genes Dev. V. 24 2556 2010
PubMed-ID: 21078819  |  Reference-DOI: 10.1101/GAD.603510

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 14-253
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: TOLUENE TOLERANCE PUMP TTGGHI OPERON REPRESSOR
 
Molecule 2 - TTGV OPERATOR DNA
    Chains: X
    Engineered: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synthetic: YES
 
Molecule 3 - TTGV OPERATOR DNA
    Chains: Y
    Engineered: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABEFXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1OS2Ligand/IonOSMIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2XRO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ICLRPS51077 IclR-type HTH domain profile.TTGV_PSEPT14-76
 		  2B:14-76
F:14-76
2ICLR_EDPS51078 IclR effector binding domain profile.TTGV_PSEPT70-253
 
 
 		  4A:70-253
B:70-253
E:70-253
F:70-253

(-) Exons   (0, 0)

(no "Exon" information available for 2XRO)

(-) 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 A from PDB  Type:PROTEIN  Length:239
 aligned with TTGV_PSEPT | Q93PU6 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:239
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         
           TTGV_PSEPT    15 QVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVCLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVCSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhh...eee......eee.hhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeee.....eee......eee...hhhhhhhhhh...hhhhhh.............hhhhhhhhhhhhhhhheeeee......eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_ICLR  PDB: - UniProt: 14-76                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------ICLR_ED  PDB: A:70-253 UniProt: 70-253                                                                                                                                                   PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xro A  15 QVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVSLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVSSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with TTGV_PSEPT | Q93PU6 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:240
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
           TTGV_PSEPT    14 IQVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVCLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVCSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee......eee.hhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeee.....eee......eee...hhhhhhhhhh.hhhhhh...............hhhhhhhhhh......eeeeeeeee..eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_ICLR  PDB: B:14-76 UniProt: 14-76                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------ICLR_ED  PDB: B:70-253 UniProt: 70-253                                                                                                                                                   PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xro B  14 IQVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVSLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVSSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253


Chain E from PDB  Type:PROTEIN  Length:239
 aligned with TTGV_PSEPT | Q93PU6 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:239
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         
           TTGV_PSEPT    15 QVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVCLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVCSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhh...eee......eee.hhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeee.....eee......eee...hhhhhhhhhh...hhhhhh.............hhhhhhhhhhhhhhhheeeee......eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_ICLR  PDB: - UniProt: 14-76                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------ICLR_ED  PDB: E:70-253 UniProt: 70-253                                                                                                                                                   PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xro E  15 QVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVSLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVSSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         


Chain F from PDB  Type:PROTEIN  Length:240
 aligned with TTGV_PSEPT | Q93PU6 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:240
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
           TTGV_PSEPT    14 IQVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVCLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVCSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee......eee.hhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeee.....eee......eee...hhhhhhhhhh.hhhhhh...............hhhhhhhhhh......eeeeeeeee..eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_ICLR  PDB: F:14-76 UniProt: 14-76                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------ICLR_ED  PDB: F:70-253 UniProt: 70-253                                                                                                                                                   PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xro F  14 IQVIARAASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQLINQAQTDILSLVKPYLRSLAEELDESVSLASLAGDKIYVLDRIVSERELRVVFPIGINVPAAATAAGKVLLAALPDETLQAALGEQLPVLTSNTLGRKALVKQLSEVRQSGVASDLDEHIDGVSSFATLLDTYLGYYSLAIVMPSSRASKQSDLIKKALLQSKLNIERAIGR 253
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253


Chain X from PDB  Type:DNA  Length:42
                                                                          
                 2xro X   1 GAGTATCACATAATGCTACACTCTACCGCATTACGATTCAGC  42
                                    10        20        30        40  


Chain Y from PDB  Type:DNA  Length:43
                                                                           
                 2xro Y   1 GCTGAATCGTAATGCGGTAGAGTGTAGCATTATGTGATACTCT  43
                                    10        20        30        40
   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 2XRO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,E,F   (TTGV_PSEPT | Q93PU6)
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/Swiss-Prot
        TTGV_PSEPT | Q93PU6: 2xrn

(-) Related Entries Specified in the PDB File

2xrn CRYSTAL STRUCTURE OF TTGV