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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RTP:NRB COMPLEX FROM BACILLUS SUBTILIS
 
Authors :  J. P. Vivian, C. J. Porter, J. A. Wilce, M. C. J. Wilce
Date :  26 Feb 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,D,E,F,G,I,J
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  F,G,I,J  (1x)
Keywords :  Protein-Dna Complex, 'Winged'-Helix Protein, Dna Replication Termination, Replication Fork Arrest, Replication-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Vivian, C. J. Porter, J. A. Wilce, M. C. J. Wilce
An Asymmetric Structure Of The Bacillus Subtilis Replicatio Terminator Protein In Complex With Dna
J. Mol. Biol. V. 370 481 2007
PubMed-ID: 17521668  |  Reference-DOI: 10.1016/J.JMB.2007.02.067

(-) Compounds

Molecule 1 - REPLICATION TERMINATION PROTEIN
    Chains: A, B, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-9
    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
 
Molecule 2 - DNA (5'- D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP *DAP*DGP*DTP*DC)-3')
    Chains: D, I
    Engineered: YES
    Other Details: THE B SITE SEQUENCE OF TERI
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DC P*DAP*DTP*DAP*DG)-3')
    Chains: E, J
    Engineered: YES
    Other Details: THE B SITE SEQUENCE OF TERI
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABDEFGIJ
Biological Unit 1 (1x): ABDE    
Biological Unit 2 (1x):     FGIJ

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2EFW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EFW)

(-) Sequences/Alignments

Asymmetric 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 d2efwa_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeeee.........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw 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 d2efwa_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeeee.........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw 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 d2efwb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw 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 d2efwb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh......hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeee.......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw B   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain D from PDB  Type:DNA  Length:19
                                                   
                 2efw D   3 ATGTACCAAATGTTCAGTC  21
                                    12         


Chain E from PDB  Type:DNA  Length:19
                                                   
                 2efw E   1 GACTGAACATTTGGTACAT  19
                                    10         


Chain F 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 d2efwf_ F: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwF00 F:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhh...eeeeeee.......eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw F   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain F 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 d2efwf_ F: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwF00 F:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhh...eeeeeee.......eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw F   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain G from PDB  Type:PROTEIN  Length:108
 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 d2efwg_ G: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwG00 G:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhhhhhhh.ee..ee.-------.ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw G   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK-------EVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        |-      | 87        97       107       117     
                                                                                               76      84                                      


Chain G from PDB  Type:PROTEIN  Length:108
 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 d2efwg_ G: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2efwG00 G:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.......hhhhhhhhh.......hhhhhhhhhhhhhhhh.ee..ee.-------.ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2efw G   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK-------EVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        |-      | 87        97       107       117     
                                                                                               76      84                                      


Chain I from PDB  Type:DNA  Length:19
                                                   
                 2efw I   3 ATGTACCAAATGTTCAGTC  21
                                    12         


Chain J from PDB  Type:DNA  Length:19
                                                   
                 2efw J   1 GACTGAACATTTGGTACAT  19
                                    10
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,F,G   (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,F,G   (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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  2efw
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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 1f4k 1j0r 2dpd 2dpu 2dqr
        RTP_BACSU | P0CI76: 1bm9 1f4k 1j0r 2dpd 2dpu 2dqr

(-) Related Entries Specified in the PDB File

1bm9 THIS IS THE WILD-TYPE APO-RTP STRUCTURE
1f4k THIS IS A SIMILAR RTP/DNA COMPLEX EXCEPT WITH A SYMMETRIC DNA SEQUENCE
1j0r THIS IS THE APO RTP.C110S STRUCTURE