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(-) Description

Title :  CRYSTAL STRUCTURE OF TOXT FROM VIBRIO CHOLERAE O395
 
Authors :  M. J. Lowden, F. J. Kull
Date :  19 Feb 09  (Deposition) - 23 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Cupin, Helix-Turn-Helix, Arac Family, Activator, Dna-Binding, Transcription, Transcription Regulation, Virulence, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lowden, K. Skorupski, M. Pellegrini, M. G. Chiorazzo, R. K. Taylor, F. J. Kull
Structure Of Vibrio Cholerae Toxt Reveals A Mechanism For Fatty Acid Regulation Of Virulence Genes.
Proc. Natl. Acad. Sci. Usa V. 107 2860 2010
PubMed-ID: 20133655  |  Reference-DOI: 10.1073/PNAS.0915021107

(-) Compounds

Molecule 1 - TCP PILUS VIRULENCE REGULATORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: TXB1
    Expression System Strain: BL21 (DE3) CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TCPN, TOXT, VC0395_A0363
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 345073
    Strain: O395

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PAM1Ligand/IonPALMITOLEIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:12 , TYR A:20 , LYS A:31 , LYS A:230 , MET A:259 , TYR A:266 , MET A:269 , HOH A:401BINDING SITE FOR RESIDUE PAM A 5975

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_ARAC_FAMILY_2PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.TCPN_VIBC3172-269  1A:172-269
2HTH_ARAC_FAMILY_1PS00041 Bacterial regulatory proteins, araC family signature.TCPN_VIBC3221-263  1A:221-263

(-) Exons   (0, 0)

(no "Exon" information available for 3GBG)

(-) 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:260
 aligned with TCPN_VIBC3 | A5F384 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:270
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
           TCPN_VIBC3     4 KKSFQTNVYRMSKFDTYIFNNLYINDYKMFWIDSGIAKLIDKNCLVSYEINSSSIILLKKNSIQRFSLTSLSDENINVSVITISDSFIRSLKSYILGDLMIRNLYSENKDLLLWNCEHNDIAVLSEVVNGFREINYSDEFLKVFFSGFFSKVEKKYNSIFITDDLDAMEKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYSISLMKTGEFKIKQIAYQSGFASVSYFSTVFKSTMNVAPSEYLFMLTGV 273
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeeeee....eeeee....eeeee....eeeee...eeeee....eeeeeeee.....eeeeeeeehhhhhhhhhhhh..----------...eeeee...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_ARAC_FAMILY_2  PDB: A:172-269 UniProt: 172-269                                                ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_ARAC_FAMILY_1  PDB: A:221-263          ---------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gbg A   4 KKSFQTNVYRMSKFDTYIFNNLYINDYKMFWIDSGIAKLIDKNCLVSYEINSSSIILLKKNSIQRFSLTSLSDENINVSVITISDSFIRSLKSYILG----------NKDLLLWNCEHNDIAVLSEVVNGFREINYSDEFLKVFFSGFFSKVEKKYNSIFITDDLDAMEKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYSISLMKTGEFKIKQIAYQSGFASVSYFSTVFKSTMNVAPSEYLFMLTGV 273
                                    13        23        33        43        53        63        73        83        93      |  -       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
                                                                                                                          100        111
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  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 3GBG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TCPN_VIBC3 | A5F384)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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
        TCPN_VIBC3 | A5F384: 5suw

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