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(-) Description

Title :  E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY
 
Authors :  D. Hargreaves, D. W. Rice, S. E. Sedelnikova, P. J. Artymiuk, R. G. Lloyd, J. B. Rafferty
Date :  11 May 98  (Deposition) - 24 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.00
Chains :  Asym./Biol. Unit :  A,B,C,D,J,K,L,M
Keywords :  Dna-Binding, Branch Migration, Holliday Junction, Ruv, Complex Dna-Binding Protein/Dna, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Hargreaves, D. W. Rice, S. E. Sedelnikova, P. J. Artymiuk, R. G. Lloyd, J. B. Rafferty
Crystal Structure Of E. Coli Ruva With Bound Dna Holliday Junction At 6 A Resolution.
Nat. Struct. Biol. V. 5 441 1998
PubMed-ID: 9628481  |  Reference-DOI: 10.1038/NSB0698-441
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
    Chains: J, K, L, M
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - HOLLIDAY JUNCTION DNA HELICASE RUVA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: RUVA
    Expression System Plasmid: PAM159
    Expression System Strain: BL21
    Expression System Taxid: 469008
    Expression System Variant: DE3
    Organism Scientific: ESCHERICHIA COLI BL21(DE3)
    Organism Taxid: 469008
    Strain: BL21
    Variant: DE3

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDJKLM

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BDX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BDX)

(-) 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:190
 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 d1bdxa3 A:1-64 DNA helicase RuvA subunit, N-terminal domain     d1bdxa2 A:65-142 DNA helicase RuvA subunit, middle domain                     -------------d1bdxa1 A:156-203                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................................................................................................................-------------................................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdx A   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTP-------------TDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |       -     | 160       170       180       190       200   
                                                                                                                                                                       142           156                                               


Chain B from PDB  Type:PROTEIN  Length:190
 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 d1bdxb3 B:1-64 DNA helicase RuvA subunit, N-terminal domain     d1bdxb2 B:65-142 DNA helicase RuvA subunit, middle domain                     -------------d1bdxb1 B:156-203                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................................................................................................................-------------................................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdx B   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTP-------------TDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |       -     | 160       170       180       190       200   
                                                                                                                                                                       142           156                                               


Chain C from PDB  Type:PROTEIN  Length:190
 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 d1bdxc3 C:1-64 DNA helicase RuvA subunit, N-terminal domain     d1bdxc2 C:65-142 DNA helicase RuvA subunit, middle domain                     -------------d1bdxc1 C:156-203                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................................................................................................................-------------................................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdx C   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTP-------------TDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |       -     | 160       170       180       190       200   
                                                                                                                                                                       142           156                                               


Chain D from PDB  Type:PROTEIN  Length:190
 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 d1bdxd3 D:1-64 DNA helicase RuvA subunit, N-terminal domain     d1bdxd2 D:65-142 DNA helicase RuvA subunit, middle domain                     -------------d1bdxd1 D:156-203                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................................................................................................................................-------------................................................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bdx D   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTP-------------TDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |       -     | 160       170       180       190       200   
                                                                                                                                                                       142           156                                               


Chain J from PDB  Type:DNA  Length:16
                                                
                 1bdx J   2 GCATGCATATGCATGC  17
                                    11      


Chain K from PDB  Type:DNA  Length:16
                                                
                 1bdx K   2 GCATGCATATGCATGC  17
                                    11      


Chain L from PDB  Type:DNA  Length:16
                                                
                 1bdx L   2 GCATGCATATGCATGC  17
                                    11      


Chain M from PDB  Type:DNA  Length:16
                                                
                 1bdx M   2 GCATGCATATGCATGC  17
                                    11
   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, 12)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1BDX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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 | P0A809: 1c7y 1cuk 1d8l 1hjp

(-) Related Entries Specified in the PDB File

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