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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX
 
Authors :  J. A. Wilce, J. P. Vivian, A. F. Hastings, G. Otting, R. H. A. Folmer, I. G. Duggin, R. G. Wake, M. C. J. Wilce
Date :  08 Jun 00  (Deposition) - 08 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Winged-Helix Protein-Dna Complex, Replication And Termination, Fork Arrest Mechanism, Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Wilce, J. P. Vivian, A. F. Hastings, G. Otting, R. H. Folmer, I. G. Duggin, R. G. Wake, M. C. Wilce
Structure Of The Rtp-Dna Complex And The Mechanism Of Polar Replication Fork Arrest
Nat. Struct. Biol. V. 8 206 2001
PubMed-ID: 11224562  |  Reference-DOI: 10.1038/84934
(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
    Other Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS
    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
    Other Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS
    Synthetic: YES
 
Molecule 3 - REPLICATION TERMINATION PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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 1F4K)

(-) Sites  (0, 0)

(no "Site" information available for 1F4K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F4K)

(-) Exons   (0, 0)

(no "Exon" information available for 1F4K)

(-) 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 d1f4ka_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 1f4kA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4k 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 d1f4ka_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 1f4kA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4k A   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain B 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 d1f4kb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 1f4kB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee...........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4k B   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain B 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 d1f4kb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 1f4kB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee...........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4k B   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain D from PDB  Type:DNA  Length:21
                                                     
                 1f4k D   1 CTATGAACATAATGTTCATAG  21
                                    10        20 


Chain E from PDB  Type:DNA  Length:21
                                                     
                 1f4k E   1 CTATGAACATTATGTTCATAG  21
                                    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  (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 1F4K)

(-) Gene Ontology  (2, 4)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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  RTP_BACSU | P0CI76
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1bm9 1BM9 IS THE UNCOMPLEXED FORM OF THE PROTEIN