RECU_BACSU
ID RECU_BACSU Reviewed; 206 AA.
AC P39792;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Holliday junction resolvase RecU;
DE EC=3.1.21.10 {ECO:0000269|PubMed:14701911};
GN Name=recU; Synonyms=prfA, yppB; OrderedLocusNames=BSU22310;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7814321; DOI=10.1128/jb.177.2.326-335.1995;
RA Popham D.L., Setlow P.;
RT "Cloning, nucleotide sequence, and mutagenesis of the Bacillus subtilis
RT ponA operon, which codes for penicillin-binding protein (PBP) 1 and a PBP-
RT related factor.";
RL J. Bacteriol. 177:326-335(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=8760912; DOI=10.1099/13500872-142-8-2005;
RA Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D.,
RA Serror P.;
RT "Sequence analysis of the Bacillus subtilis chromosome region between the
RT serA and kdg loci cloned in a yeast artificial chromosome.";
RL Microbiology 142:2005-2016(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168 / YB886 / BG214;
RX PubMed=9642195; DOI=10.1128/jb.180.13.3405-3409.1998;
RA Fernandez S., Sorokin A., Alonso J.C.;
RT "Genetic recombination in Bacillus subtilis 168: effects of recU and recS
RT mutations on DNA repair and homologous recombination.";
RL J. Bacteriol. 180:3405-3409(1998).
RN [5]
RP CHARACTERIZATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / PS832;
RX PubMed=10692371; DOI=10.1128/jb.182.6.1650-1658.2000;
RA Pedersen L.B., Setlow P.;
RT "Penicillin-binding protein-related factor A is required for proper
RT chromosome segregation in Bacillus subtilis.";
RL J. Bacteriol. 182:1650-1658(2000).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168 / YB886 / BG214;
RX PubMed=11810266; DOI=10.1007/s00438-001-0616-7;
RA Carrasco B., Fernandez S., Asai K., Ogasawara N., Alonso J.C.;
RT "Effect of the recU suppressors sms and subA on DNA repair and homologous
RT recombination in Bacillus subtilis.";
RL Mol. Genet. Genomics 266:899-906(2002).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MASS SPECTROMETRY.
RX PubMed=14701911; DOI=10.1073/pnas.2533829100;
RA Ayora S., Carrasco B., Doncel E., Lurz R., Alonso J.C.;
RT "Bacillus subtilis RecU protein cleaves Holliday junctions and anneals
RT single-stranded DNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:452-457(2004).
RN [8]
RP FUNCTION.
RC STRAIN=168 / YB886 / BG214;
RX PubMed=16020779; DOI=10.1534/genetics.105.045906;
RA Sanchez H., Kidane D., Reed P., Curtis F.A., Cozar M.C., Graumann P.L.,
RA Sharples G.J., Alonso J.C.;
RT "The RuvAB branch migration translocase and RecU Holliday junction
RT resolvase are required for double-stranded DNA break repair in Bacillus
RT subtilis.";
RL Genetics 171:873-883(2005).
RN [9]
RP INTERACTION WITH RECA, MUTAGENESIS OF LYS-56 AND ARG-71, SUBUNIT,
RP SS-DNA-BINDING, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / YB886 / BG214;
RX PubMed=18684995; DOI=10.1093/nar/gkn500;
RA Canas C., Carrasco B., Ayora S., Alonso J.C.;
RT "The RecU Holliday junction resolvase acts at early stages of homologous
RT recombination.";
RL Nucleic Acids Res. 36:5242-5249(2008).
RN [10]
RP CHARACTERIZATION, THE N-TERMINUS IS ESSENTIAL, SUBUNIT, DNA-BINDING,
RP INTERACTION WITH RUVB, AND MUTAGENESIS OF 1-MET--GLY-32; PRO-5 AND ARG-31.
RC STRAIN=168 / YB886 / BG214;
RX PubMed=19422832; DOI=10.1016/j.jmb.2009.04.065;
RA Carrasco B., Canas C., Sharples G.J., Alonso J.C., Ayora S.;
RT "The N-terminal region of the RecU Holliday junction resolvase is essential
RT for homologous recombination.";
RL J. Mol. Biol. 390:1-9(2009).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS,
RP FUNCTION, MUTAGENESIS OF GLU-36; ASP-88; ASP-99 AND GLU-101, AND SUBUNIT.
RX PubMed=16154091; DOI=10.1016/j.str.2005.05.011;
RA McGregor N., Ayora S., Sedelnikova S., Carrasco B., Alonso J.C., Thaw P.,
RA Rafferty J.;
RT "The structure of Bacillus subtilis RecU Holliday junction resolvase and
RT its role in substrate selection and sequence-specific cleavage.";
RL Structure 13:1341-1351(2005).
CC -!- FUNCTION: Has at least 2 separable functions; Holliday junction
CC resolution with generation of monomeric chromosomes, and modulation of
CC RecA activity. Endonuclease that resolves Holliday junction
CC intermediates in genetic recombination. Cleaves mobile four-strand
CC junctions by introducing symmetrical nicks in paired strands. Promotes
CC annealing of linear ssDNA with homologous dsDNA. Required for DNA
CC repair, homologous recombination and chromosome segregation. Partially
CC inhibits the hydrolysis of dATP or rATP by RecA. Holliday junction
CC resolution is stimulated by RuvB. {ECO:0000269|PubMed:14701911,
CC ECO:0000269|PubMed:16020779, ECO:0000269|PubMed:16154091}.
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 Evidence={ECO:0000269|PubMed:14701911};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:14701911};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:14701911};
CC -!- SUBUNIT: Homodimer. Interacts with RuvB. {ECO:0000269|PubMed:16154091,
CC ECO:0000269|PubMed:18684995, ECO:0000269|PubMed:19422832}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- MASS SPECTROMETRY: Mass=23945; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:14701911};
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene have a greatly increased
CC sensitivity to DNA damaging agents, 25-fold decreased plasmid
CC transformation and only slightly reduced chromosomal DNA transformation
CC (PubMed:10692371). They form anucleate cells 100-times more frequently
CC than wild-type cells during normal growth (PubMed:18684995). DNA
CC damaging agent sensitivity is partially suppressed by disruption of
CC radA and fin (also called sms and subA respectively) (PubMed:11810266).
CC {ECO:0000269|PubMed:10692371, ECO:0000269|PubMed:11810266,
CC ECO:0000269|PubMed:18684995, ECO:0000269|PubMed:9642195}.
CC -!- SIMILARITY: Belongs to the RecU family. {ECO:0000305}.
CC -!- CAUTION: Recombination protein U, a short form proposed to initiate
CC from Met-33, which is equivalent to RecU-delta1-32, is not detected in
CC vivo, and would not be functional. The name is misleading and should no
CC longer be used. {ECO:0000305}.
CC -!- CAUTION: Was originally named prfA (Penicillin-binding protein-related
CC factor A, PBP-related factor A) due to its proximity to the ponA gene;
CC this name is misleading and should no longer be used.
CC {ECO:0000305|PubMed:7814321}.
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DR EMBL; U11883; AAA64946.1; -; Genomic_DNA.
DR EMBL; L47838; AAB38460.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14147.1; -; Genomic_DNA.
DR PIR; I40528; I40528.
DR RefSeq; NP_390112.1; NC_000964.3.
DR RefSeq; WP_004399067.1; NZ_JNCM01000036.1.
DR PDB; 1RZN; X-ray; 2.30 A; A/B=2-206.
DR PDB; 1ZP7; X-ray; 2.25 A; A/B=1-206.
DR PDB; 5FDK; X-ray; 3.21 A; A/B/C/D=1-199.
DR PDBsum; 1RZN; -.
DR PDBsum; 1ZP7; -.
DR PDBsum; 5FDK; -.
DR AlphaFoldDB; P39792; -.
DR SMR; P39792; -.
DR STRING; 224308.BSU22310; -.
DR PaxDb; P39792; -.
DR EnsemblBacteria; CAB14147; CAB14147; BSU_22310.
DR GeneID; 939039; -.
DR KEGG; bsu:BSU22310; -.
DR PATRIC; fig|224308.179.peg.2435; -.
DR eggNOG; COG3331; Bacteria.
DR OMA; TDYNGIY; -.
DR PhylomeDB; P39792; -.
DR BioCyc; BSUB:BSU22310-MON; -.
DR BRENDA; 3.1.21.10; 658.
DR EvolutionaryTrace; P39792; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008821; F:crossover junction endodeoxyribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0007059; P:chromosome segregation; IEA:UniProtKB-UniRule.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR GO; GO:0006281; P:DNA repair; IMP:CACAO.
DR Gene3D; 3.40.1350.10; -; 1.
DR HAMAP; MF_00130; RecU; 1.
DR InterPro; IPR004612; Resolv_RecU.
DR InterPro; IPR011335; Restrct_endonuc-II-like.
DR InterPro; IPR011856; tRNA_endonuc-like_dom_sf.
DR Pfam; PF03838; RecU; 1.
DR PIRSF; PIRSF037785; RecU; 1.
DR SUPFAM; SSF52980; SSF52980; 1.
DR TIGRFAMs; TIGR00648; recU; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA damage; DNA recombination; DNA repair;
KW DNA-binding; Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome.
FT CHAIN 1..206
FT /note="Holliday junction resolvase RecU"
FT /id="PRO_0000212296"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 10..34
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 86
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 88
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 101
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 120
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT SITE 103
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT MUTAGEN 1..32
FT /note="Missing: Greatly increased sensitivity to DNA-
FT damaging agents, chromosome segregation defects. Binds DNA
FT but cannot cleave a Holliday junction."
FT /evidence="ECO:0000269|PubMed:19422832"
FT MUTAGEN 5
FT /note="P->A: No phenotype."
FT /evidence="ECO:0000269|PubMed:19422832"
FT MUTAGEN 31
FT /note="R->A: Greatly increased sensitivity to DNA-damaging
FT agents, chromosome segregation defects. Binds DNA and is
FT able to cleave a Holliday junction."
FT /evidence="ECO:0000269|PubMed:19422832"
FT MUTAGEN 36
FT /note="E->A,Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16154091"
FT MUTAGEN 56
FT /note="K->A: Cleaves Holliday junctions, no interaction
FT with RecA, greatly increased sensitivity to DNA-damaging
FT agents."
FT /evidence="ECO:0000269|PubMed:18684995"
FT MUTAGEN 71
FT /note="R->A: Cleaves Holliday junctions, no interaction
FT with RecA, greatly increased sensitivity to DNA-damaging
FT agents."
FT /evidence="ECO:0000269|PubMed:18684995"
FT MUTAGEN 88
FT /note="D->A,N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16154091"
FT MUTAGEN 99
FT /note="D->A: Reduces Holliday junction resolution activity
FT 6-fold."
FT /evidence="ECO:0000269|PubMed:16154091"
FT MUTAGEN 101
FT /note="E->A: Loss of Holliday junction resolution
FT activity."
FT /evidence="ECO:0000269|PubMed:16154091"
FT STRAND 16..20
FT /evidence="ECO:0007829|PDB:5FDK"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 53..56
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:5FDK"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:5FDK"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:5FDK"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 96..104
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 118..129
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 133..140
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 143..148
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 149..157
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 169..175
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:1ZP7"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:1ZP7"
FT HELIX 189..197
FT /evidence="ECO:0007829|PDB:1ZP7"
SQ SEQUENCE 206 AA; 23959 MW; 104C7989E8ED88E7 CRC64;
MIRYPNGKTF QPKHSVSSQN SQKRAPSYSN RGMTLEDDLN ETNKYYLTNQ IAVIHKKPTP
VQIVNVHYPK RSAAVIKEAY FKQSSTTDYN GIYKGRYIDF EAKETKNKTS FPLQNFHDHQ
IEHMKQVKAQ DGICFVIISA FDQVYFLEAD KLFYFWDRKE KNGRKSIRKD ELEETAYPIS
LGYAPRIDYI SIIEQLYFSP SSGAKG
