YDJA_BACSU
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 03-AUG-2022, entry version 93.
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; Firmicutes; 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 / NCIMB
RC 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 / NCIMB
RC 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 / NCIMB
RC 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; O34303; -.
DR PRIDE; O34303; -.
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 OMA; FANGEWR; -.
DR BioCyc; BSUB:BSU06110-MON; -.
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
