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(-) Description

Title :  MECHANISTIC BASIS OF PLASMID-SPECIFIC DNA BINDING OF THE F PLASMID REGULATORY PROTEIN, TRAM
 
Authors :  Y. Peng, J. Lu, J. Wong, R. A. Edwards, L. S. Frost, J. N. M. Glover
Date :  24 Jun 14  (Deposition) - 24 Sep 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,P,Q
Keywords :  Rhh Motif, Dna Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Peng, J. Lu, J. J. Wong, R. A. Edwards, L. S. Frost, J. N. Mark Glover
Mechanistic Basis Of Plasmid-Specific Dna Binding Of The F Plasmid Regulatory Protein, Tram.
J. Mol. Biol. V. 426 3783 2014
PubMed-ID: 25284757  |  Reference-DOI: 10.1016/J.JMB.2014.09.018

(-) Compounds

Molecule 1 - RELAXOSOME PROTEIN TRAM
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentF-TRAM RHH DOMAIN, UNP RESIDUES 2-54
    GeneTRAM, ECOK12F071
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
 
Molecule 2 - SBMA DNA1
    ChainsP
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES
 
Molecule 3 - SBMA DNA2
    ChainsQ
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit ABCDEFGHPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4QPQ)

(-) Sites  (0, 0)

(no "Site" information available for 4QPQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QPQ)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:27 -Ala A:28
2Gly B:27 -Ala B:28
3Gly C:27 -Ala C:28
4Gly D:27 -Ala D:28
5Gly E:27 -Ala E:28
6Gly F:27 -Ala F:28
7Gly G:27 -Ala G:28
8Gly H:27 -Ala H:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QPQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QPQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4QPQ)

(-) 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:50
                                                                                 
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  4qpq A  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHE 51
                                    11        21        31        41        51

Chain B from PDB  Type:PROTEIN  Length:52
                                                                                   
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  4qpq B  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQ 53
                                    11        21        31        41        51  

Chain C from PDB  Type:PROTEIN  Length:52
                                                                                   
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  4qpq C  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQ 53
                                    11        21        31        41        51  

Chain D from PDB  Type:PROTEIN  Length:52
                                                                                   
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  4qpq D  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQ 53
                                    11        21        31        41        51  

Chain E from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  4qpq E  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHE 51
                                    11        21        31        41        51

Chain F from PDB  Type:PROTEIN  Length:52
                                                                                   
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  4qpq F  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQ 53
                                    11        21        31        41        51  

Chain G from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  4qpq G  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHE 51
                                    11        21        31        41        51

Chain H from PDB  Type:PROTEIN  Length:51
                                                                                  
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  4qpq H  2 AKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEA 52
                                    11        21        31        41        51 

Chain P from PDB  Type:DNA  Length:28
                                                           
                  4qpq P  1 ATACCGCTAGGGGCGCTGCTAGCGGTGC 28
                                    10        20        

Chain Q from PDB  Type:DNA  Length:28
                                                           
                  4qpq Q  1 GCACCGCTAGCAGCGCCCCTAGCGGTAT 28
                                    10        20        

   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 4QPQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QPQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QPQ)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4qpq)
 
  Sites
(no "Sites" information available for 4qpq)
 
  Cis Peptide Bonds
    Gly A:27 - Ala A:28   [ RasMol ]  
    Gly B:27 - Ala B:28   [ RasMol ]  
    Gly C:27 - Ala C:28   [ RasMol ]  
    Gly D:27 - Ala D:28   [ RasMol ]  
    Gly E:27 - Ala E:28   [ RasMol ]  
    Gly F:27 - Ala F:28   [ RasMol ]  
    Gly G:27 - Ala G:28   [ RasMol ]  
    Gly H:27 - Ala H:28   [ RasMol ]  
 

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  TRAM1_ECOLI | P10026
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRAM1_ECOLI | P100262g7o 2g9e 3d8a 4qpo

(-) Related Entries Specified in the PDB File

4qpo