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Protein

Crossover junction endodeoxyribonuclease RusA

Gene

rusA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of CC dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC.

Catalytic activityi

Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).

Cofactori

Mg2+CuratedNote: Binds 1 Mg2+ ion per subunit.Curated

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi70 – 701MagnesiumCurated
Metal bindingi72 – 721MagnesiumCurated
Metal bindingi91 – 911MagnesiumCurated

GO - Molecular functioni

  1. crossover junction endodeoxyribonuclease activity Source: EcoCyc
  2. magnesium ion binding Source: InterPro
  3. recombination hotspot binding Source: EcoCyc

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. DNA recombination Source: UniProtKB-KW
  3. DNA repair Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6306-MONOMER.
ECOL316407:JW0538-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Crossover junction endodeoxyribonuclease RusA (EC:3.1.22.4)
Alternative name(s):
Holliday junction nuclease RusA
Holliday junction resolvase
Gene namesi
Name:rusA
Synonyms:rus, ybcP
Ordered Locus Names:b0550, JW0538
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG20283. rusA.

Subcellular locationi

GO - Cellular componenti

  1. Holliday junction resolvase complex Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi16 – 161R → Q: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi17 – 171Y → L: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi19 – 191R → Q: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi58 – 581R → Q: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi68 – 681R → Q: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi69 – 691R → Q or A: Loss of ability to promote DNA repair. Great loss of Holliday junction resolvase activity. No effect on DNA binding. 1 Publication
Mutagenesisi70 – 701D → N: Reduces junction resolution 80-fold. No effect on DNA binding. 2 Publications
Mutagenesisi72 – 721D → N: Loss of ability to resolve junctions. No effect on DNA binding. 1 Publication
Mutagenesisi73 – 731N → A: Slight reduction in ability to promote DNA repair. Great reduction in Holliday junction resolution activity. 1 Publication
Mutagenesisi76 – 761K → Q: Loss of ability to promote DNA repair. Loss of Holliday junction resolvase activity. No effect on DNA binding. 1 Publication
Mutagenesisi76 – 761K → R: Loss of ability to promote DNA repair. Less than 2% activity of Holliday junction resolvase. No effect on DNA binding. 1 Publication
Mutagenesisi80 – 801D → N: Slight reduction in ability to resolve junctions. No effect on DNA binding. 1 Publication
Mutagenesisi87 – 871F → Y or V: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi90 – 901D → N: Slight reduction in ability to resolve junctions. No effect on DNA binding. 1 Publication
Mutagenesisi91 – 911D → N: Loss of ability to resolve junctions. No effect on DNA binding. 1 Publication
Mutagenesisi101 – 1011K → Q: No effect on ability to promote DNA repair. 1 Publication
Mutagenesisi111 – 1111E → Q: No effect on resolvase activity or DNA binding. 1 Publication
Mutagenesisi116 – 1161E → Q: No effect on resolvase activity or DNA binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 120120Crossover junction endodeoxyribonuclease RusAPRO_0000192004Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP0AG74.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

BioGridi849560. 4 interactions.
DIPiDIP-16988N.
IntActiP0AG74. 1 interaction.
STRINGi511145.b0550.

Structurei

Secondary structure

1
120
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Helixi14 – 174Combined sources
Beta strandi18 – 236Combined sources
Beta strandi25 – 273Combined sources
Helixi29 – 4416Combined sources
Beta strandi55 – 628Combined sources
Beta strandi64 – 674Combined sources
Helixi72 – 8413Combined sources
Beta strandi87 – 893Combined sources
Helixi91 – 933Combined sources
Beta strandi94 – 1029Combined sources
Beta strandi109 – 1168Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q8RX-ray1.90A/B1-120[»]
2H8CX-ray3.10A/B/C/D1-120[»]
2H8EX-ray1.20A1-120[»]
ProteinModelPortaliP0AG74.
SMRiP0AG74. Positions 1-118.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AG74.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni13 – 164DNA binding
Regioni66 – 738DNA binding

Sequence similaritiesi

Belongs to the RusA family.Curated

Phylogenomic databases

eggNOGiCOG4570.
HOGENOMiHOG000119986.
InParanoidiP0AG74.
KOiK01160.
OMAiIHYISDW.
OrthoDBiEOG66HVH9.

Family and domain databases

Gene3Di3.30.1330.70. 1 hit.
InterProiIPR016281. Endonuclease_RusA.
IPR008822. Endonuclease_RusA-like.
[Graphical view]
PfamiPF05866. RusA. 1 hit.
[Graphical view]
PIRSFiPIRSF001007. RusA. 1 hit.
SUPFAMiSSF103084. SSF103084. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AG74-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNTYSITLPW PPSNNRYYRH NRGRTHVSAE GQAYRDNVAR IIKNAMLDIG
60 70 80 90 100
LAMPVKIRIE CHMPDRRRRD LDNLQKAAFD ALTKAGFWLD DAQVVDYRVV
110 120
KMPVTKGGRL ELTITEMGNE
Length:120
Mass (Da):13,846
Last modified:December 20, 2005 - v1
Checksum:i38401669E8819EA6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92587 Genomic DNA. Translation: CAA63321.1.
U82598 Genomic DNA. Translation: AAB40746.1.
U00096 Genomic DNA. Translation: AAC73651.1.
AP009048 Genomic DNA. Translation: BAE76325.1.
PIRiS66590.
RefSeqiNP_415082.1. NC_000913.3.
YP_488837.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73651; AAC73651; b0550.
BAE76325; BAE76325; BAE76325.
GeneIDi12932535.
945174.
KEGGiecj:Y75_p0535.
eco:b0550.
PATRICi32116262. VBIEscCol129921_0571.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X92587 Genomic DNA. Translation: CAA63321.1.
U82598 Genomic DNA. Translation: AAB40746.1.
U00096 Genomic DNA. Translation: AAC73651.1.
AP009048 Genomic DNA. Translation: BAE76325.1.
PIRiS66590.
RefSeqiNP_415082.1. NC_000913.3.
YP_488837.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q8RX-ray1.90A/B1-120[»]
2H8CX-ray3.10A/B/C/D1-120[»]
2H8EX-ray1.20A1-120[»]
ProteinModelPortaliP0AG74.
SMRiP0AG74. Positions 1-118.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi849560. 4 interactions.
DIPiDIP-16988N.
IntActiP0AG74. 1 interaction.
STRINGi511145.b0550.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73651; AAC73651; b0550.
BAE76325; BAE76325; BAE76325.
GeneIDi12932535.
945174.
KEGGiecj:Y75_p0535.
eco:b0550.
PATRICi32116262. VBIEscCol129921_0571.

Organism-specific databases

EchoBASEiEB4170.
EcoGeneiEG20283. rusA.

Phylogenomic databases

eggNOGiCOG4570.
HOGENOMiHOG000119986.
InParanoidiP0AG74.
KOiK01160.
OMAiIHYISDW.
OrthoDBiEOG66HVH9.

Enzyme and pathway databases

BioCyciEcoCyc:G6306-MONOMER.
ECOL316407:JW0538-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AG74.
PROiP0AG74.

Gene expression databases

GenevestigatoriP0AG74.

Family and domain databases

Gene3Di3.30.1330.70. 1 hit.
InterProiIPR016281. Endonuclease_RusA.
IPR008822. Endonuclease_RusA-like.
[Graphical view]
PfamiPF05866. RusA. 1 hit.
[Graphical view]
PIRSFiPIRSF001007. RusA. 1 hit.
SUPFAMiSSF103084. SSF103084. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82."
    Mahdi A.A., Sharples G.J., Mandal T.N., Lloyd R.G.
    J. Mol. Biol. 257:561-573(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions."
    Sharples G.J., Chan S.N., Mahdi A.A., Whitby M.C., Lloyd R.G.
    EMBO J. 13:6133-6142(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-9, CHARACTERIZATION.
  6. "Sequence specificity and biochemical characterization of the RusA Holliday junction resolvase of Escherichia coli."
    Chan S.N., Harris L., Bolt E.L., Whitby M.C., Lloyd R.G.
    J. Biol. Chem. 272:14873-14882(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, SUBUNIT.
  7. "Structural recognition and distortion by the DNA junction-resolving enzyme RusA."
    Giraud-Panis M.-J.E., Lilley D.M.J.
    J. Mol. Biol. 278:117-133(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE SPECIFICITY, DNA-BINDING, MUTAGENESIS OF ASP-70.
  8. "Identification of three aspartic acid residues essential for catalysis by the RusA holliday junction resolvase."
    Bolt E.L., Sharples G.J., Lloyd R.G.
    J. Mol. Biol. 286:403-415(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-70; ASP-72; ASP-80; ASP-90; ASP-91; GLU-111 AND GLU-116.
  9. "Analysis of conserved basic residues associated with DNA binding (Arg69) and catalysis (Lys76) by the RusA holliday junction resolvase."
    Bolt E.L., Sharples G.J., Lloyd R.G.
    J. Mol. Biol. 304:165-176(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-16; TYR-17; ARG-19; ARG-58; ARG-68; ARG-69; ASN-73; LYS-76; PHE-87 AND LYS-101.
  10. "The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold."
    Rafferty J.B., Bolt E.L., Muranova T.A., Sedelnikova S.E., Leonard P., Pasquo A., Baker P.J., Rice D.W., Sharples G.J., Lloyd R.G.
    Structure 11:1557-1567(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SUBUNIT.
  11. "RusA Holliday junction resolvase: DNA complex structure -- insights into selectivity and specificity."
    Macmaster R., Sedelnikova S., Baker P.J., Bolt E.L., Lloyd R.G., Rafferty J.B.
    Nucleic Acids Res. 34:5577-5584(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF MUTANT ASN-70 IN COMPLEX WITH DNA, SUBUNIT.

Entry informationi

Entry nameiRUSA_ECOLI
AccessioniPrimary (citable) accession number: P0AG74
Secondary accession number(s): P40116, Q2MBN1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: January 7, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Encoded by the cryptic lambdoid prophage DLP12. Normally not expressed. Complete suppression of ruv mutations by RusA is dependent on the activity of RecG.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.