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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN MUTANT RTP.E39K.R42Q
 
Authors :  J. P. Vivian, J. A. Wilce, M. C. J. Wilce
Date :  29 May 06  (Deposition) - 29 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Replication, Winged-Helix, Rtp, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Vivian, J. A. Wilce, M. C. J. Wilce
Crystal Structure Of The Replication Terminator Protein Mutant Rtp. E39K. R42Q
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATION TERMINATION PROTEIN
    Chains: A, B, C, D
    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 Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DQR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DQR)

(-) 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:107
 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 d2dqra_ A: Replication terminator protein (RTP)                                                                       SCOP domains
               CATH domains 2dqrA00 A:6-122 'winged helix' repressor DNA binding domain                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee----------...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr A   6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQI----------EVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    15        25        35        45        55        65       | -        85        95       105       115       
                                                                                              73         84                                      


Chain A from PDB  Type:PROTEIN  Length:107
 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 d2dqra_ A: Replication terminator protein (RTP)                                                                       SCOP domains
               CATH domains 2dqrA00 A:6-122 'winged helix' repressor DNA binding domain                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee----------...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr A   6 RSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQI----------EVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    15        25        35        45        55        65       | -        85        95       105       115       
                                                                                              73         84                                      


Chain B from PDB  Type:PROTEIN  Length:112
 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 d2dqrb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dqrB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..ee...hhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee.....---...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr B   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEG---QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77 |   |  87        97       107       117     
                                                                                                  79  83                                       


Chain B from PDB  Type:PROTEIN  Length:112
 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 d2dqrb_ B: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dqrB00 B:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..ee...hhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee.....---...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr B   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEG---QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    17        27        37        47        57        67        77 |   |  87        97       107       117     
                                                                                                  79  83                                       


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with RTP_BACPZ | E0TY12 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:112
                                    20        30        40        50        60        70        80        90       100       110       120  
            RTP_BACPZ    11 FLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dqrc_ C: Replication terminator protein (RTP)                                                                  SCOP domains
               CATH domains 2dqrC00 C:11-122 'winged helix' repressor DNA binding domain                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee.------..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr C  11 FLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK------QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    20        30        40        50        60        70     |   -  |     90       100       110       120  
                                                                                            76     83                                       


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with RTP_BACSU | P0CI76 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:112
                                    20        30        40        50        60        70        80        90       100       110       120  
            RTP_BACSU    11 FLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
               SCOP domains d2dqrc_ C: Replication terminator protein (RTP)                                                                  SCOP domains
               CATH domains 2dqrC00 C:11-122 'winged helix' repressor DNA binding domain                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee.------..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr C  11 FLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK------QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    20        30        40        50        60        70     |   -  |     90       100       110       120  
                                                                                            76     83                                       


Chain D from PDB  Type:PROTEIN  Length:109
 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 d2dqrd_ D: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dqrD00 D:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhh..eeeeee.------..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr D   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK------QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    17        27        37        47        57        67        |-     |  87        97       107       117     
                                                                                               76     83                                       


Chain D from PDB  Type:PROTEIN  Length:109
 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 d2dqrd_ D: Replication terminator protein (RTP)                                                                     SCOP domains
               CATH domains 2dqrD00 D:8-122 'winged helix' repressor DNA binding domain                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhh..eeeeee.------..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2dqr D   8 STGFLVKQRAFLKLYMITMTEQERLYGLKLLKVLQSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVK------QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF 122
                                    17        27        37        47        57        67        |-     |  87        97       107       117     
                                                                                               76     83
   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 2DQR)

(-) Gene Ontology  (2, 4)

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

(-) Related Entries Specified in the PDB File

1bm9 WILD-TYPE STRUCTURE
1f4k MUTANT STRUCTURE BOUND TO SYMMETRIC B-SITE DNA