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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF COLE2-P9 REP IN COMPLEX WITH THE REPLICATION ORIGIN
 
Authors :  H. Itou, M. Yagura, T. Itoh, Y. Shirakihara
Date :  31 Jul 12  (Deposition) - 31 Jul 13  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Helix-Turn-Helix, Specific Dna-Binding And Unwinding Of Dna Duplex, Cytosol, Replication Initiator Protein, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itou, M. Yagura, Y. Shirakihara, T. Itoh
Structural Basis For Replication Origin Unwinding By An Initiator-Primase Of Plasmid Cole2-P9: Duplex Dna Unwinding By A Single Protein
J. Biol. Chem. V. 290 3601 2015
PubMed-ID: 25538245  |  Reference-DOI: 10.1074/JBC.M114.595645

(-) Compounds

Molecule 1 - REP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDIG DOMAIN
    Gene: REP
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REPLICATION INITIATOR COLE2-REP
 
Molecule 2 - DNA (5'- D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP *C)-3')
    Chains: C, E
    Engineered: YES
    Other Details: SYNTHETIC OLIGO DNA
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP *T)-3')
    Chains: D, F
    Engineered: YES
    Other Details: SYNTHETIC OLIGO DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:172 , HIS A:173 , HIS A:174 , ARG A:175BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREHIS B:171 , HIS B:172 , HIS B:173 , HIS B:174 , ARG B:175 , HOH B:407BINDING SITE FOR RESIDUE SO4 B 301
3AC3SOFTWAREHIS A:173 , HIS B:174 , ASN B:176 , TYR B:177 , DG F:13BINDING SITE FOR RESIDUE SO4 B 302
4AC4SOFTWAREPRO B:222 , ARG B:226BINDING SITE FOR RESIDUE SO4 B 303
5AC5SOFTWAREGLN A:193 , GLY A:194 , TRP B:186 , ARG B:208BINDING SITE FOR RESIDUE SO4 B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VW4)

(-) Exons   (0, 0)

(no "Exon" information available for 3VW4)

(-) 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:122
 aligned with Q06B24_ECOLX | Q06B24 from UniProtKB/TrEMBL  Length:297

    Alignment length:122
                                   179       189       199       209       219       229       239       249       259       269       279       289  
         Q06B24_ECOLX   170 NYGLGRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSPAECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGISRATYYRKLKC 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vw4 A 170 HHHHHRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSPAECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGISRATYYRKLKC 291
                                   179       189       199       209       219       229       239       249       259       269       279       289  


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q06B24_ECOLX | Q06B24 from UniProtKB/TrEMBL  Length:297

    Alignment length:120
                                   180       190       200       210       220       230       240       250       260       270       280       290
         Q06B24_ECOLX   171 YGLGRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSPAECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGISRATYYRKLK 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vw4 B 171 HHHHRNYHLFEKVRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSPAECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGTKSKRAAVPTSARSLKPWEALGISRATYYRKLK 290
                                   180       190       200       210       220       230       240       250       260       270       280       290


Chain C from PDB  Type:DNA  Length:20
                                                    
                 3vw4 C   3 AATGAGACCAGATAAGCCTT  22
                                    12        22


Chain D from PDB  Type:DNA  Length:20
                                                    
                 3vw4 D  13 GATAAGGCTTATCTGGTCTC  32
                                    22        32


Chain E from PDB  Type:DNA  Length:21
                                                     
                 3vw4 E   3 AATGAGACCAGATAAGCCTTA  23
                                    12        22 


Chain F from PDB  Type:DNA  Length:20
                                                    
                 3vw4 F  13 GATAAGGCTTATCTGGTCTC  32
                                    22        32
   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  (0, 0)

(no "SCOP Domain" information available for 3VW4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VW4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3VW4)

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