ID   RUSA_ECOLI              Reviewed;         120 AA.
AC   P0AG74; P40116; Q2MBN1;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   20-DEC-2005, sequence version 1.
DT   24-JAN-2024, entry version 126.
DE   RecName: Full=Crossover junction endodeoxyribonuclease RusA;
DE            EC=3.1.21.10;
DE   AltName: Full=Holliday junction nuclease RusA;
DE   AltName: Full=Holliday junction resolvase;
GN   Name=rusA; Synonyms=rus, ybcP; OrderedLocusNames=b0550, JW0538;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=8648624; DOI=10.1006/jmbi.1996.0185;
RA   Mahdi A.A., Sharples G.J., Mandal T.N., Lloyd R.G.;
RT   "Holliday junction resolvases encoded by homologous rusA genes in
RT   Escherichia coli K-12 and phage 82.";
RL   J. Mol. Biol. 257:561-573(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RA   Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA   Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA   Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT   "Sequence of minutes 4-25 of Escherichia coli.";
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   PROTEIN SEQUENCE OF 1-9, AND CHARACTERIZATION.
RX   PubMed=7813450; DOI=10.1002/j.1460-2075.1994.tb06960.x;
RA   Sharples G.J., Chan S.N., Mahdi A.A., Whitby M.C., Lloyd R.G.;
RT   "Processing of intermediates in recombination and DNA repair:
RT   identification of a new endonuclease that specifically cleaves Holliday
RT   junctions.";
RL   EMBO J. 13:6133-6142(1994).
RN   [6]
RP   CHARACTERIZATION, AND SUBUNIT.
RX   PubMed=9169457; DOI=10.1074/jbc.272.23.14873;
RA   Chan S.N., Harris L., Bolt E.L., Whitby M.C., Lloyd R.G.;
RT   "Sequence specificity and biochemical characterization of the RusA Holliday
RT   junction resolvase of Escherichia coli.";
RL   J. Biol. Chem. 272:14873-14882(1997).
RN   [7]
RP   CLEAVAGE SPECIFICITY, DNA-BINDING, AND MUTAGENESIS OF ASP-70.
RX   PubMed=9571038; DOI=10.1006/jmbi.1998.1681;
RA   Giraud-Panis M.-J.E., Lilley D.M.J.;
RT   "Structural recognition and distortion by the DNA junction-resolving enzyme
RT   RusA.";
RL   J. Mol. Biol. 278:117-133(1998).
RN   [8]
RP   MUTAGENESIS OF ASP-70; ASP-72; ASP-80; ASP-90; ASP-91; GLU-111 AND GLU-116.
RX   PubMed=9973560; DOI=10.1006/jmbi.1998.2499;
RA   Bolt E.L., Sharples G.J., Lloyd R.G.;
RT   "Identification of three aspartic acid residues essential for catalysis by
RT   the RusA holliday junction resolvase.";
RL   J. Mol. Biol. 286:403-415(1999).
RN   [9]
RP   MUTAGENESIS OF ARG-16; TYR-17; ARG-19; ARG-58; ARG-68; ARG-69; ASN-73;
RP   LYS-76; PHE-87 AND LYS-101.
RX   PubMed=11080453; DOI=10.1006/jmbi.2000.4196;
RA   Bolt E.L., Sharples G.J., Lloyd R.G.;
RT   "Analysis of conserved basic residues associated with DNA binding (Arg69)
RT   and catalysis (Lys76) by the RusA holliday junction resolvase.";
RL   J. Mol. Biol. 304:165-176(2000).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND SUBUNIT.
RX   PubMed=14656440; DOI=10.1016/j.str.2003.11.004;
RA   Rafferty J.B., Bolt E.L., Muranova T.A., Sedelnikova S.E., Leonard P.,
RA   Pasquo A., Baker P.J., Rice D.W., Sharples G.J., Lloyd R.G.;
RT   "The structure of Escherichia coli RusA endonuclease reveals a new Holliday
RT   junction DNA binding fold.";
RL   Structure 11:1557-1567(2003).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF MUTANT ASN-70 IN COMPLEX WITH DNA,
RP   AND SUBUNIT.
RX   PubMed=17028102; DOI=10.1093/nar/gkl447;
RA   Macmaster R., Sedelnikova S., Baker P.J., Bolt E.L., Lloyd R.G.,
RA   Rafferty J.B.;
RT   "RusA Holliday junction resolvase: DNA complex structure -- insights into
RT   selectivity and specificity.";
RL   Nucleic Acids Res. 34:5577-5584(2006).
CC   -!- FUNCTION: Endonuclease that resolves Holliday junction intermediates
CC       made during homologous genetic recombination and DNA repair. Exhibits
CC       sequence and structure-selective cleavage of four-way DNA junctions,
CC       where it introduces symmetrical nicks in two strands of the same
CC       polarity at the 5' side of CC dinucleotides. Corrects the defects in
CC       genetic recombination and DNA repair associated with inactivation of
CC       ruvAB or ruvC.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage at a junction such as a reciprocal
CC         single-stranded crossover between two homologous DNA duplexes
CC         (Holliday junction).; EC=3.1.21.10;
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000305};
CC       Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000305};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:14656440,
CC       ECO:0000269|PubMed:17028102, ECO:0000269|PubMed:9169457}.
CC   -!- MISCELLANEOUS: Encoded by the cryptic lambdoid prophage DLP12. Normally
CC       not expressed. Complete suppression of ruv mutations by RusA is
CC       dependent on the activity of RecG.
CC   -!- SIMILARITY: Belongs to the RusA family. {ECO:0000305}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; X92587; CAA63321.1; -; Genomic_DNA.
DR   EMBL; U82598; AAB40746.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC73651.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76325.1; -; Genomic_DNA.
DR   PIR; S66590; S66590.
DR   RefSeq; NP_415082.1; NC_000913.3.
DR   RefSeq; WP_001099712.1; NZ_LN832404.1.
DR   PDB; 1Q8R; X-ray; 1.90 A; A/B=1-120.
DR   PDB; 2H8C; X-ray; 3.10 A; A/B/C/D=1-120.
DR   PDB; 2H8E; X-ray; 1.20 A; A=1-120.
DR   PDBsum; 1Q8R; -.
DR   PDBsum; 2H8C; -.
DR   PDBsum; 2H8E; -.
DR   AlphaFoldDB; P0AG74; -.
DR   SMR; P0AG74; -.
DR   BioGRID; 4261529; 59.
DR   BioGRID; 849560; 4.
DR   DIP; DIP-16988N; -.
DR   IntAct; P0AG74; 1.
DR   STRING; 511145.b0550; -.
DR   PaxDb; 511145-b0550; -.
DR   EnsemblBacteria; AAC73651; AAC73651; b0550.
DR   GeneID; 945174; -.
DR   KEGG; ecj:JW0538; -.
DR   KEGG; eco:b0550; -.
DR   PATRIC; fig|1411691.4.peg.1727; -.
DR   EchoBASE; EB4170; -.
DR   eggNOG; COG4570; Bacteria.
DR   HOGENOM; CLU_139466_0_2_6; -.
DR   InParanoid; P0AG74; -.
DR   OMA; YISDWGK; -.
DR   OrthoDB; 73971at2; -.
DR   PhylomeDB; P0AG74; -.
DR   BioCyc; EcoCyc:G6306-MONOMER; -.
DR   BRENDA; 3.1.21.10; 2026.
DR   EvolutionaryTrace; P0AG74; -.
DR   PRO; PR:P0AG74; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0008821; F:crossover junction DNA endonuclease activity; IDA:EcoCyc.
DR   GO; GO:0000400; F:four-way junction DNA binding; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   Gene3D; 3.30.1330.70; Holliday junction resolvase RusA; 1.
DR   InterPro; IPR016281; Endonuclease_RusA.
DR   InterPro; IPR008822; Endonuclease_RusA-like.
DR   InterPro; IPR036614; RusA-like_sf.
DR   Pfam; PF05866; RusA; 1.
DR   PIRSF; PIRSF001007; RusA; 1.
DR   SUPFAM; SSF103084; Holliday junction resolvase RusA; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; DNA damage; DNA recombination;
KW   DNA repair; Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW   Reference proteome.
FT   CHAIN           1..120
FT                   /note="Crossover junction endodeoxyribonuclease RusA"
FT                   /id="PRO_0000192004"
FT   REGION          13..16
FT                   /note="DNA-binding"
FT   REGION          66..73
FT                   /note="DNA-binding"
FT   BINDING         70
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000305"
FT   BINDING         72
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000305"
FT   BINDING         91
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000305"
FT   MUTAGEN         16
FT                   /note="R->Q: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         17
FT                   /note="Y->L: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         19
FT                   /note="R->Q: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         58
FT                   /note="R->Q: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         68
FT                   /note="R->Q: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         69
FT                   /note="R->Q,A: Loss of ability to promote DNA repair. Great
FT                   loss of Holliday junction resolvase activity. No effect on
FT                   DNA binding."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         70
FT                   /note="D->N: Reduces junction resolution 80-fold. No effect
FT                   on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:9571038,
FT                   ECO:0000269|PubMed:9973560"
FT   MUTAGEN         72
FT                   /note="D->N: Loss of ability to resolve junctions. No
FT                   effect on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   MUTAGEN         73
FT                   /note="N->A: Slight reduction in ability to promote DNA
FT                   repair. Great reduction in Holliday junction resolution
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         76
FT                   /note="K->Q: Loss of ability to promote DNA repair. Loss of
FT                   Holliday junction resolvase activity. No effect on DNA
FT                   binding."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         76
FT                   /note="K->R: Loss of ability to promote DNA repair. Less
FT                   than 2% activity of Holliday junction resolvase. No effect
FT                   on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         80
FT                   /note="D->N: Slight reduction in ability to resolve
FT                   junctions. No effect on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   MUTAGEN         87
FT                   /note="F->Y,V: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         90
FT                   /note="D->N: Slight reduction in ability to resolve
FT                   junctions. No effect on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   MUTAGEN         91
FT                   /note="D->N: Loss of ability to resolve junctions. No
FT                   effect on DNA binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   MUTAGEN         101
FT                   /note="K->Q: No effect on ability to promote DNA repair."
FT                   /evidence="ECO:0000269|PubMed:11080453"
FT   MUTAGEN         111
FT                   /note="E->Q: No effect on resolvase activity or DNA
FT                   binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   MUTAGEN         116
FT                   /note="E->Q: No effect on resolvase activity or DNA
FT                   binding."
FT                   /evidence="ECO:0000269|PubMed:9973560"
FT   STRAND          3..9
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   HELIX           14..17
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          18..23
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          25..27
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   HELIX           29..44
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          55..62
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          64..67
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   HELIX           72..84
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          87..89
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   HELIX           91..93
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          94..102
FT                   /evidence="ECO:0007829|PDB:2H8E"
FT   STRAND          109..116
FT                   /evidence="ECO:0007829|PDB:2H8E"
SQ   SEQUENCE   120 AA;  13846 MW;  38401669E8819EA6 CRC64;
     MNTYSITLPW PPSNNRYYRH NRGRTHVSAE GQAYRDNVAR IIKNAMLDIG LAMPVKIRIE
     CHMPDRRRRD LDNLQKAAFD ALTKAGFWLD DAQVVDYRVV KMPVTKGGRL ELTITEMGNE
//