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(-) Description

Title :  E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX
 
Authors :  M. Ariyoshi, T. Nishino, H. Iwasaki, H. Shinagawa, K. Morikawa
Date :  03 Apr 00  (Deposition) - 21 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,B,C,D,E,F,G,H,I  (4x)
Keywords :  Helix-Hairpin-Helix, Protein-Dna Complex, Homologous Recombination, Holliday Junction, Recombination/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Ariyoshi, T. Nishino, H. Iwasaki, H. Shinagawa, K. Morikawa
Crystal Structure Of The Holliday Junction Dna In Complex With A Single Ruva Tetramer.
Proc. Natl. Acad. Sci. Usa V. 97 8257 2000
PubMed-ID: 10890893  |  Reference-DOI: 10.1073/PNAS.140212997
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION DNA HELICASE RUVA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - DNA (5'- D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)- 3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'- D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 4 - DNA (5'- D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)- 3')
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 5 - DNA (5'- D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
    ChainsE
    EngineeredYES
    SyntheticYES
 
Molecule 6 - DNA (5'- D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)- 3')
    ChainsF
    EngineeredYES
    SyntheticYES
 
Molecule 7 - DNA (5'- D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
    ChainsG
    EngineeredYES
    SyntheticYES
 
Molecule 8 - DNA (5'- D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)- 3')
    ChainsH
    EngineeredYES
    SyntheticYES
 
Molecule 9 - DNA (5'- D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
    ChainsI
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit ABCDEFGHI
Biological Unit 1 (4x)ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1C7Y)

(-) Sites  (0, 0)

(no "Site" information available for 1C7Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C7Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:14 -Pro A:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1C7Y)

(-) 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:199
 aligned with RUVA_ECOLI | P0A809 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
           RUVA_ECOLI     1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
               SCOP domains d1c7ya3 A:1-64 DNA helicase RuvA subunit, N-terminal domain     d1c7ya2 A:65-150 DNA helicase RuvA subunit, middle domain                             ----d1c7ya1 A:155-203                                 SCOP domains
               CATH domains 1c7yA01 A:1-66 Nucleic acid-binding proteins                      1c7yA02 A:67-142 5' to 3' exonuclease, C-terminal subdomain                 -------------1c7yA03 A:156-203                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeee..eeeeee.hhhhhh.......eeeeeeee........eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhh............hhhhhhhh----..hhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c7y A   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADLVLTS----ATDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    |  160       170       180       190       200   
                                                                                                                                                                               150  155                                                

Chain B from PDB  Type:DNA  Length:13
                                             
                 1c7y B 401 AAGTTGGGATTGT 413
                                   410   

Chain C from PDB  Type:DNA  Length:12
                                            
                 1c7y C 501 CTGTGTGTAAGC 512
                                   510  

Chain D from PDB  Type:DNA  Length:13
                                             
                 1c7y D 401 GCTTACACACAGA 413
                                   410   

Chain E from PDB  Type:DNA  Length:12
                                            
                 1c7y E 501 GGTTAGGGTGAA 512
                                   510  

Chain F from PDB  Type:DNA  Length:13
                                             
                 1c7y F 401 TTCACCCTAACCA 413
                                   410   

Chain G from PDB  Type:DNA  Length:12
                                            
                 1c7y G 501 GACACACATTCG 512
                                   510  

Chain H from PDB  Type:DNA  Length:13
                                             
                 1c7y H 401 CGAATGTGTGTCT 413
                                   410   

Chain I from PDB  Type:DNA  Length:12
                                            
                 1c7y I 501 CAATCCCAACTT 512
                                   510  

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C7Y)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (RUVA_ECOLI | P0A809)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0009378    four-way junction helicase activity    Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000725    recombinational repair    A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
cellular component
    GO:0009379    Holliday junction helicase complex    A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.
    GO:0048476    Holliday junction resolvase complex    A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RUVA_ECOLI | P0A8091bdx 1cuk 1d8l 1hjp

(-) Related Entries Specified in the PDB File

1hjp CONTAINS THE SAME PROTEIN WITHOUT DNA