ID   YDJA_BACSU              Reviewed;         465 AA.
AC   O34303; Q797C8;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   27-MAR-2024, entry version 100.
DE   RecName: Full=Type II restriction enzyme BsuMI component YdjA {ECO:0000303|PubMed:12654995};
DE            Short=R.BsuM;
DE            Short=R.BsuMI;
DE            EC=3.1.21.4 {ECO:0000269|PubMed:2830465};
DE   AltName: Full=Endonuclease BsuMI component YdjA;
DE   AltName: Full=Type-2 restriction enzyme BsuMI component YdjA;
GN   Name=ydjA; OrderedLocusNames=BSU06110;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 /
RC   NCIMB 3610 / NRRL NRS-744 / VKM B-501;
RX   PubMed=9455482; DOI=10.1093/dnares/4.5.335;
RA   Kasahara Y., Nakai S., Ogasawara N., Yata K., Sadaie Y.;
RT   "Sequence analysis of the groESL-cotA region of the Bacillus subtilis
RT   genome, containing the restriction/modification system genes.";
RL   DNA Res. 4:335-339(1997).
RN   [2]
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   [3]
RP   FUNCTION, AND DNA TARGET SEQUENCE.
RC   STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 /
RC   NCIMB 3610 / NRRL NRS-744 / VKM B-501;
RX   PubMed=2830465; DOI=10.1007/bf00338412;
RA   Bron S., Janniere L., Ehrlich S.D.;
RT   "Restriction and modification in Bacillus subtilis Marburg 168: target
RT   sites and effects on plasmid transformation.";
RL   Mol. Gen. Genet. 211:186-189(1988).
RN   [4]
RP   SUBUNIT, DEVELOPMENTAL STAGE, INDUCTION, OPERON STRUCTURE, AND DISRUPTION
RP   PHENOTYPE.
RC   STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 /
RC   NCIMB 3610 / NRRL NRS-744 / VKM B-501;
RX   PubMed=11751814; DOI=10.1128/jb.184.2.381-389.2002;
RA   Ohshima H., Matsuoka S., Asai K., Sadaie Y.;
RT   "Molecular organization of intrinsic restriction and modification genes
RT   BsuM of Bacillus subtilis Marburg.";
RL   J. Bacteriol. 184:381-389(2002).
RN   [5]
RP   NOMENCLATURE, AND SUBTYPE.
RX   PubMed=12654995; DOI=10.1093/nar/gkg274;
RA   Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A.,
RA   Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K.,
RA   Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S.,
RA   Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A.,
RA   Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S.,
RA   Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V.,
RA   Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E.,
RA   Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W.,
RA   Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.;
RT   "A nomenclature for restriction enzymes, DNA methyltransferases, homing
RT   endonucleases and their genes.";
RL   Nucleic Acids Res. 31:1805-1812(2003).
RN   [6]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168 / PY79;
RX   PubMed=32324221; DOI=10.1093/nar/gkaa266;
RA   Nye T.M., van Gijtenbeek L.A., Stevens A.G., Schroeder J.W., Randall J.R.,
RA   Matthews L.A., Simmons L.A.;
RT   "Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine
RT   modifications at non-palindromic recognition sites in Bacillus subtilis.";
RL   Nucleic Acids Res. 48:5332-5348(2020).
CC   -!- FUNCTION: A P subtype restriction enzyme that recognizes the double-
CC       stranded sequence 5'-CTCGAG-3'; the cleavage site is unknown.
CC       {ECO:0000269|PubMed:2830465, ECO:0000269|PubMed:32324221,
CC       ECO:0000303|PubMed:12654995}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage of DNA to give specific double-
CC         stranded fragments with terminal 5'-phosphates.; EC=3.1.21.4;
CC         Evidence={ECO:0000269|PubMed:2830465};
CC   -!- SUBUNIT: BsuMI restriction activity requires YdiR, YdiS and YdjA.
CC       {ECO:0000269|PubMed:11751814}.
CC   -!- DEVELOPMENTAL STAGE: Not expressed during sporulation.
CC       {ECO:0000269|PubMed:11751814}.
CC   -!- INDUCTION: Constitutively expressed during exponential growth. Encoded
CC       in an operon with ydiR and ydiS. {ECO:0000269|PubMed:11751814}.
CC   -!- DISRUPTION PHENOTYPE: Not essential; its disruption results in
CC       increased transformation by plasmid DNA carrying multiple BsuMI target
CC       sequences (PubMed:11751814). Triple deletion ydiO-ydiP-ydjA leads to
CC       loss of susceptibility to MspJI, which only digests C-methylated DNA
CC       (PubMed:32324221). {ECO:0000269|PubMed:11751814,
CC       ECO:0000269|PubMed:32324221}.
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DR   EMBL; AB007637; BAA22755.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB12430.1; -; Genomic_DNA.
DR   PIR; E69788; E69788.
DR   RefSeq; NP_388492.1; NC_000964.3.
DR   RefSeq; WP_003234050.1; NZ_JNCM01000032.1.
DR   AlphaFoldDB; O34303; -.
DR   STRING; 224308.BSU06110; -.
DR   REBASE; 156235; Bsu16045ORF661P.
DR   REBASE; 162054; R1.BsuBS38ORF585P.
DR   REBASE; 619; BsuMI.
DR   PaxDb; 224308-BSU06110; -.
DR   EnsemblBacteria; CAB12430; CAB12430; BSU_06110.
DR   GeneID; 939884; -.
DR   KEGG; bsu:BSU06110; -.
DR   PATRIC; fig|224308.179.peg.662; -.
DR   eggNOG; ENOG502ZBUR; Bacteria.
DR   InParanoid; O34303; -.
DR   OrthoDB; 9811025at2; -.
DR   BioCyc; BSUB:BSU06110-MONOMER; -.
DR   PRO; PR:O34303; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0009036; F:type II site-specific deoxyribonuclease activity; IEA:UniProtKB-EC.
DR   GO; GO:0009307; P:DNA restriction-modification system; IEA:UniProtKB-KW.
DR   InterPro; IPR018579; Restrct_endonuc_II_LlaJI.
DR   Pfam; PF09563; RE_LlaJI; 1.
PE   1: Evidence at protein level;
KW   Endonuclease; Hydrolase; Nuclease; Reference proteome; Restriction system.
FT   CHAIN           1..465
FT                   /note="Type II restriction enzyme BsuMI component YdjA"
FT                   /id="PRO_0000379883"
SQ   SEQUENCE   465 AA;  54336 MW;  DE93019E964B0E65 CRC64;
     MDKSSKFFFE DQKYNKERIV RVLGGNLALL KSKGILYEDS SGDLIFNYVG VISNGRNVIF
     ILPKYCNRHL DEHSKRTLFN KLLKIFKKYS GLNKSRESDY FVSELDSDEV SDFMIADYLL
     NDFSLNGYYQ KKFTEYEIDG EGIIDWSKTV NEITPVFSKG VPYYFSTYNE VVQKDEYHLI
     VKIHKWALSK YFNDFGVILG FTGLEFDKSC DGMKILDYAD FFGSVINKEI VNTYVDRDVK
     LLKALKTAID REENQFSKRP TLSLYGTKYF HRVWEEVCKT VFSHVNEYVK KISRPNWINF
     TDIEVNKEKK TLEPDIIKAF EYRSKEYFLI LDAKYYNINF DGKKLEGNPG VEDITKQLLY
     DKALEKLSRG KTKHNAFLFP SSNSTNTFKV FGSVDFDFLD IAAVTLVYIS AEQVYNLYLE
     NKTFSTDDLF KFVSEINKSK KRHSVITSTL YGNMFLFTKR LSDKN
//