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(-) Description

Title :  E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III
 
Authors :  T. Nishino, H. Iwasaki, M. Kataoka, M. Ariyoshi, T. Fujita, H. Shinagawa, K. Morikawa
Date :  25 Oct 99  (Deposition) - 03 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Ob-Fold, Helix-Hairpin-Helix Motif, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nishino, H. Iwasaki, M. Kataoka, M. Ariyoshi, T. Fujita, H. Shinagawa, K. Morikawa
Modulation Of Ruvb Function By The Mobile Domain Iii Of The Holliday Junction Recognition Protein Ruva.
J. Mol. Biol. V. 298 407 2000
PubMed-ID: 10772859  |  Reference-DOI: 10.1006/JMBI.2000.3675
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNH2 REGION
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1D8L)

(-) Sites  (0, 0)

(no "Site" information available for 1D8L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D8L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:14 -Pro A:15
2Pro B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D8L)

(-) Exons   (0, 0)

(no "Exon" information available for 1D8L)

(-) 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:140
 aligned with RUVA_ECOLI | P0A809 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           RUVA_ECOLI     1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLF 140
               SCOP domains d1d8la2 A:1-64 DNA helicase RuvA subunit, N-terminal domain     d1d8la1 A:65-140 DNA helicase RuvA subunit, middle domain                    SCOP domains
               CATH domains 1d8lA02 A:1-65 Nucleic acid-binding proteins                     -1d8lA01 A:67-135 5' to 3' exonuclease, C-terminal subdomain          ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeee..eeeeee.hhhhhhh......eeeeeeeeeee..eeeeeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8l A   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLF 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with RUVA_ECOLI | P0A809 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           RUVA_ECOLI     1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLF 140
               SCOP domains d1d8lb2 B:1-64 DNA helicase RuvA subunit, N-terminal domain     d1d8lb1 B:65-140 DNA helicase RuvA subunit, middle domain                    SCOP domains
               CATH domains 1d8lB02 B:1-65 Nucleic acid-binding proteins                     -1d8lB01 B:67-135 5' to 3' exonuclease, C-terminal subdomain          ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeee..eeeeee.hhhhhhhh.....eeeeeeeeeee..eeeeeee.hhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8l B   1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLF 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D8L)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1c7y 1cuk 1hjp

(-) Related Entries Specified in the PDB File

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