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(-) Description

Title :  PPS10 PLASMID DNA REPLICATION INITIATOR PROTEIN REPA. REPLICATION INACTIVE, DIMERIC N-TERMINAL DOMAIN.
 
Authors :  R. Giraldo, C. Fernandez-Tornero, P. R. Evans, R. Diaz-Orejas, A. Romero
Date :  11 Mar 03  (Deposition) - 29 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Binding Protein, Winged-Helix, Pps10 Plasmid, Replication Initiator Dimer. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Giraldo, C. Fernandez-Tornero, P. R. Evans, R. Diaz-Orejas, A. Romero
A Conformational Switch Between Transcriptional Repression And Replication Initiation In Repa Dimerization Domain
Nat. Struct. Biol. V. 10 496 2003
PubMed-ID: 12825085  |  Reference-DOI: 10.1038/NSB0703-496
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICATION PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: SG22097
    Expression System Plasmid: PRG-RECA-NHIS
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN DIMER, RESIDUES 2-133
    Organism Common: PSEUDOMONAS SAVASTANOI
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. SAVASTANOI
    Organism Taxid: 29438
    Other Details: PPS10 PLASMID DNA REPLICATION INITIATOR, REPLICATION INACTIVE, DIMERIC SPECIES
    Synonym: REPA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2HG8Ligand/IonMERCURY (II) ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:104 , CYS A:106 , BEZ A:1134BINDING SITE FOR RESIDUE HG A1133
02AC2SOFTWARECYS A:29 , SER A:32BINDING SITE FOR RESIDUE HG A1135
03AC3SOFTWARETHR A:114 , HIS A:118BINDING SITE FOR RESIDUE HG A1136
04AC4SOFTWARESER A:32 , HIS A:123BINDING SITE FOR RESIDUE HG A1137
05AC5SOFTWARELYS A:62 , HIS A:63 , LYS A:85BINDING SITE FOR RESIDUE PO4 A1138
06AC6SOFTWAREGLN B:104 , CYS B:106 , BEZ B:1134BINDING SITE FOR RESIDUE HG B1133
07AC7SOFTWARECYS B:29 , SER B:32BINDING SITE FOR RESIDUE HG B1135
08AC8SOFTWARETHR B:114 , HIS B:118BINDING SITE FOR RESIDUE HG B1136
09AC9SOFTWAREHIS B:123BINDING SITE FOR RESIDUE HG B1137
10BC1SOFTWAREARG A:49 , GLN A:104 , HG A:1133 , HIS B:123 , LYS B:124BINDING SITE FOR RESIDUE BEZ A1134
11BC2SOFTWAREHIS A:123 , LYS A:124 , GLN B:104 , HG B:1133BINDING SITE FOR RESIDUE BEZ B1134

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1HKQ)

(-) 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:125
 aligned with Q52546_PSESX | Q52546 from UniProtKB/TrEMBL  Length:231

    Alignment length:125
                                    18        28        38        48        58        68        78        88        98       108       118       128     
         Q52546_PSESX     9 QSNKLIESSHTLTLNEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAYAALDDAATKLFNRDIRRYVKGKVVERMRWVFHVKYREGQGCVELGFSPTIIPHLTMLHKEFTSYQLK 133
               SCOP domains d1hkqa_ A: Replication protein A, repA                                                                                        SCOP domains
               CATH domains 1hkqA00 A:8-132 'winged helix' repressor DNA binding domain                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhh..........eeeeeehhhhhhhh.....hhhhhhhhhhhhhhhh.eeeee..eeeeeee..eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkq A   8 QSNKLIESSHTLTLNEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAYAALDDAATKLFNRDIRRYVKGKVVERMRWVFHVKYREGQGCVELGFSPTIIPHLTMLHKEFTSYQLK 132
                                    17        27        37        47        57        67        77        87        97       107       117       127     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with Q52546_PSESX | Q52546 from UniProtKB/TrEMBL  Length:231

    Alignment length:125
                                    18        28        38        48        58        68        78        88        98       108       118       128     
         Q52546_PSESX     9 QSNKLIESSHTLTLNEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAYAALDDAATKLFNRDIRRYVKGKVVERMRWVFHVKYREGQGCVELGFSPTIIPHLTMLHKEFTSYQLK 133
               SCOP domains d1hkqb_ B: Replication protein A, repA                                                                                        SCOP domains
               CATH domains 1hkqB00 B:8-132 'winged helix' repressor DNA binding domain                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhh..........eeeeeehhhhhhhh.....hhhhhhhhhhhhhhhh.eeeee..eeeeeee..eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkq B   8 QSNKLIESSHTLTLNEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAYAALDDAATKLFNRDIRRYVKGKVVERMRWVFHVKYREGQGCVELGFSPTIIPHLTMLHKEFTSYQLK 132
                                    17        27        37        47        57        67        77        87        97       107       117       127
   Legend:   → Mismatch (orange background)
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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, 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 1HKQ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q52546_PSESX | Q52546)
molecular function
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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