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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REPLICATION TERMINATION PROTEIN IN COMPLEX WITH A PSEUDOSYMMETRIC B-SITE
 
Authors :  J. P. Vivian, J. Wilce, M. C. J. Wilce
Date :  09 May 06  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.17
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Winged-Helix Protein-Dna Complex, Replication Termination, Fork Arrest Mechanism, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Vivian, J. Wilce, M. C. J. Wilce
Crystal Structure Of The Replication Termination Protein In Complex With A Pseudosymmetric B-Site
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP *AP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP *AP*G)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - REPLICATION TERMINATION PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-3
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RTP
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: REPLICATION TERMINATOR PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DPD)

(-) Sites  (0, 0)

(no "Site" information available for 2DPD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DPD)

(-) Exons   (0, 0)

(no "Exon" information available for 2DPD)

(-) 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:115
 aligned with RTP_BACPZ | E0TY12 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:115
                                    17        27        37        47        57        67        77        87        97       107       117     
            RTP_BACPZ     8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dpda_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dpdA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee.............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpd A   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain A from PDB  Type:PROTEIN  Length:115
 aligned with RTP_BACSU | P0CI76 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:115
                                    17        27        37        47        57        67        77        87        97       107       117     
            RTP_BACSU     8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dpda_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dpdA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee.............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpd A   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with RTP_BACPZ | E0TY12 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:117
                                    15        25        35        45        55        65        75        85        95       105       115       
            RTP_BACPZ     6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dpdb_ B: Replication terminator protein (RTP)                                                                       SCOP domains
               CATH domains 2dpdB00 B:6-122 'winged helix' repressor DNA binding domain                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee.........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpd B   6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    15        25        35        45        55        65        75        85        95       105       115       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with RTP_BACSU | P0CI76 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:117
                                    15        25        35        45        55        65        75        85        95       105       115       
            RTP_BACSU     6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dpdb_ B: Replication terminator protein (RTP)                                                                       SCOP domains
               CATH domains 2dpdB00 B:6-122 'winged helix' repressor DNA binding domain                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee.........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpd B   6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    15        25        35        45        55        65        75        85        95       105       115       


Chain D from PDB  Type:DNA  Length:21
                                                     
                 2dpd D   1 CTATGAACATAATGTTCATAG  21
                                    10        20 


Chain E from PDB  Type:DNA  Length:21
                                                     
                 2dpd E   1 CTATGAACATTATGTTCATAG  21
                                    10        20
   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RTP_BACPZ | E0TY12)
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:0006274    DNA replication termination    The process in which DNA replication at a replication fork ceases; occurs when the replication fork reaches a specific termination site or when two replication forks meet.

Chain A,B   (RTP_BACSU | P0CI76)
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:0006274    DNA replication termination    The process in which DNA replication at a replication fork ceases; occurs when the replication fork reaches a specific termination site or when two replication forks meet.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RTP_BACPZ | E0TY12: 1bm9 1f4k 1j0r 2dpu 2dqr 2efw
        RTP_BACSU | P0CI76: 1bm9 1f4k 1j0r 2dpu 2dqr 2efw

(-) Related Entries Specified in the PDB File

1bm9 WILD-TYPE APO-STRUCTURE
1f4k THE SAME COMPLEX SOLVED IN A DIFFERENT SPACE GROUP
1j0r APO-STRUCTURE