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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REPLICATION TERMINATION PROTEIN IN COMPLEX WITH A PSEUDOSYMMETRIC 21MER B-SITE DNA
 
Authors :  J. P. Vivian, J. Wilce, M. C. J. Wilce
Date :  15 May 06  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,D,E
Biol. Unit 1:  A,D,E  (2x)
Keywords :  Protein-Dna Complex, Winged-Helix, Dna Replication, 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 21Mer B-Site Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(P*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*T)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - REPLICATION TERMINATION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3
    Expression System Strain: BL21.PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RTP
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: REPLICATION TERMINATOR PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ADE
Biological Unit 1 (2x): ADE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DPU)

(-) 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 d2dpua_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dpuA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeee...........eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpu 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 d2dpua_ A: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dpuA00 A:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeeee...........eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpu A   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77        87        97       107       117     


Chain D from PDB  Type:DNA  Length:10
                                          
                 2dpu D  12 ATGTTCATAG  21
                                    21


Chain E from PDB  Type:DNA  Length:11
                                           
                 2dpu E   1 CTATGAACATT  11
                                    10
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

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

(-) Related Entries Specified in the PDB File

1bm9 THIS IS THE WILD-TYPE APO-STRUCTURE
1f4k THIS IS THE SAME STRUCTURE SOLVED IN A DIFFERENT SPACE GROUP
1j0r THIS IS THE APO-STRUCTURE OF THE MUTANT RTP.C110S
2dpd THIS IS THE SAME STRUCTURE SOLVED IN A DIFFERENT SPACE GROUP