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(-) Description

Title :  CRYSTAL STRUCTURE OF THE QUORUM-SENSING PROTEIN TRAM FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  A. Vannini, S. Di Marco
Date :  30 Sep 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Repressor, Negative Regulator, Quorum-Sensing, Conjugation, Transcription Regulation, Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Vannini, C. Volpari, S. Di Marco
Crystal Structure Of The Quorum-Sensing Protein Tram And Its Interaction With The Transcriptional Regulator Trar
J. Biol. Chem. V. 279 24291 2004
PubMed-ID: 15044488  |  Reference-DOI: 10.1074/JBC.M401855200

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REPRESSOR TRAM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7.7
    Expression System Strain: B834
    Expression System Taxid: 562
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Other Details: SYNTHETIC GENE
    Synonym: TRAM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1UPG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UPG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UPG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UPG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UPG)

(-) Exons   (0, 0)

(no "Exon" information available for 1UPG)

(-) 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:91
 aligned with TRAM_RHIRD | Q57471 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:91
                                    21        31        41        51        61        71        81        91       101 
           TRAM_RHIRD    12 VELRPLIGLTRGLPPTDLETITIDAIRTHRRLVEKADELFQALPETYKTGQACGGPQHIRYIEASIEMHAQMSALNTLYSILGFIPKVVVN 102
               SCOP domains d1upga_ A: Transcriptional repressor TraM                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh--...... Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------eee------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1upg A  12 VELRPLIGLTRGLPPTDLETITIDAIRTHRRLVEKADELFQALPETYKTGQACGGPQHIRYIEASIEmHAQmSALNTLYSILGFIPKVVVN 102
                                    21        31        41        51        61        71       |81 |      91       101 
                                                                                              79-MSE                   
                                                                                                  83-MSE               


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with TRAM_RHIRD | Q57471 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           TRAM_RHIRD     1 MELEDANVTKKVELRPLIGLTRGLPPTDLETITIDAIRTHRRLVEKADELFQALPETYKTGQACGGPQHIRYIEASIEMHAQMSALNTLYSILGFIPKVV 100
               SCOP domains d1upgb_ B: Transcriptional repressor TraM                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Prok-TraM-1upgB01 B:1-99                                                                           - Pfam domains (1)
           Pfam domains (2) Prok-TraM-1upgB02 B:1-99                                                                           - Pfam domains (2)
         Sec.struct. author ..eee.........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1upg B   1 mELEDANVTKKVELRPLIGLTRGLPPTDLETITIDAIRTHRRLVEKADELFQALPETYKTGQACGGPQHIRYIEASIEmHAQmSALNTLYSILGFIPKVV 100
                            |       10        20        30        40        50        60        70        80  |     90       100
                            1-MSE                                                                        79-MSE                 
                                                                                                             83-MSE
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UPG)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Prok-TraM] (3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRAM_RHIRD | Q57471)
biological process
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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
        TRAM_RHIRD | Q57471: 1rfy 1us6

(-) Related Entries Specified in the PDB File

1us6 CRYSTAL STRUCTURE OF THE QUORUM-SENSING PROTEIN TRAM FROM AGROBACTERIUM TUMEFACIENS AT 1.65 ANG. RESOLUTION