YDIP_BACSU
ID YDIP_BACSU Reviewed; 389 AA.
AC O34680; Q797D0;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Type II methyltransferase M2.BsuMI {ECO:0000303|PubMed:12654995};
DE Short=M2.BsuMI {ECO:0000303|PubMed:12654995};
DE EC=2.1.1.37;
DE AltName: Full=BsuMI modification methylase subunit YdiP;
DE AltName: Full=Cytosine-specific methyltransferase M2.BsuMI;
GN Name=ydiP; OrderedLocusNames=BSU06070;
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, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=3150363; DOI=10.1016/0378-1119(88)90256-9;
RA Guha S.;
RT "DNA methyltransferase of Bacillus subtilis Marburg: purification,
RT properties and further evidence of specificity.";
RL Gene 74:77-81(1988).
RN [4]
RP 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 [5]
RP FUNCTION, 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 [6]
RP NOMENCLATURE.
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 [7]
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 methylase, recognizes the double-stranded sequence 5'-
CC YTCGAR-3', methylates C-3 on both strands, and protects the DNA from
CC cleavage by the BsuMI endonuclease. {ECO:0000269|PubMed:11751814,
CC ECO:0000269|PubMed:3150363, ECO:0000269|PubMed:32324221}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-
CC methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:13681, Rhea:RHEA-COMP:11369, Rhea:RHEA-COMP:11370,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:85452, ChEBI:CHEBI:85454; EC=2.1.1.37;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10018};
CC -!- ACTIVITY REGULATION: Somewhat inhibited by MgCl(2) and spermidine,
CC strongly inhibited by MnCl(2). {ECO:0000269|PubMed:3150363}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.6 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:3150363};
CC KM=3 nM for DNA {ECO:0000269|PubMed:3150363};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:3150363};
CC Temperature dependence:
CC Rapidly loses activity at 37 degrees Celsius in the absence of DNA.
CC {ECO:0000269|PubMed:3150363};
CC -!- SUBUNIT: Monomer (PubMed:3150363). May form a complex with YdiP, also
CC seems to be active alone (Probable). {ECO:0000269|PubMed:3150363,
CC ECO:0000305|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 ydiO and in a second with groES, groEL, ydiM and
CC ydiN. This second operon is heat-inducible.
CC {ECO:0000269|PubMed:11751814}.
CC -!- DISRUPTION PHENOTYPE: Essential for growth, it can be disrupted once
CC one of the components of the corresponding BsuMI restriction
CC endonuclease complex (AC O34303, O34885, O35025, YdjA, YdiS and YdiR
CC respectively) has been disrupted (PubMed:11751814). Triple deletions
CC ydiO-ydiP-ydiR, ydiO-ydiP-ydiS and ydiO-ydiP-ydjA lead to loss of
CC susceptibility to MspJI, which only digests C-methylated DNA
CC (PubMed:32324221). {ECO:0000269|PubMed:11751814,
CC ECO:0000269|PubMed:32324221}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
CC -!- CAUTION: The characterized enzyme was reported to be a monomer of
CC approximately 45 kDa; it is not clear whether this corresponds to YdiO,
CC YdiP or to another activity altogether. {ECO:0000305|PubMed:3150363}.
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DR EMBL; AB007637; BAA22751.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12426.1; -; Genomic_DNA.
DR PIR; A69788; A69788.
DR RefSeq; NP_388488.1; NC_000964.3.
DR RefSeq; WP_003242904.1; NZ_JNCM01000032.1.
DR AlphaFoldDB; O34680; -.
DR SMR; O34680; -.
DR STRING; 224308.BSU06070; -.
DR REBASE; 152750; M.Rsp324ORF1111P.
DR REBASE; 152763; M.Rsp541ORF1071P.
DR REBASE; 152771; M.Rsp941ORF1071P.
DR REBASE; 156236; M2.Bsu16045ORF661P.
DR REBASE; 166488; M.Nse506ORF862P.
DR REBASE; 203183; M.Bam1267ORF1949P.
DR REBASE; 251329; M2.BliADL4ORF1556P.
DR REBASE; 3613; M2.BsuMI.
DR PaxDb; O34680; -.
DR EnsemblBacteria; CAB12426; CAB12426; BSU_06070.
DR GeneID; 939876; -.
DR KEGG; bsu:BSU06070; -.
DR PATRIC; fig|224308.43.peg.637; -.
DR eggNOG; COG0270; Bacteria.
DR InParanoid; O34680; -.
DR OMA; WAVNAVP; -.
DR PhylomeDB; O34680; -.
DR BioCyc; BSUB:BSU06070-MON; -.
DR PRO; PR:O34680; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008168; F:methyltransferase activity; NAS:UniProtKB.
DR GO; GO:0032776; P:DNA methylation on cytosine; IMP:UniProtKB.
DR GO; GO:0009307; P:DNA restriction-modification system; IMP:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018117; C5_DNA_meth_AS.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR031303; C5_meth_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF00145; DNA_methylase; 2.
DR PRINTS; PR00105; C5METTRFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS00094; C5_MTASE_1; 1.
DR PROSITE; PS00095; C5_MTASE_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Reference proteome; Restriction system;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..389
FT /note="Type II methyltransferase M2.BsuMI"
FT /id="PRO_0000379885"
FT DOMAIN 1..299
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT ACT_SITE 69
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018"
SQ SEQUENCE 389 AA; 43284 MW; 16578833225AFE22 CRC64;
MKVVSLFSGI GGIELGLHQS GHTTEIFCEV DPLAKAVLSK NFPGVKIEDD INEIRELPSC
DLVAAGFPCQ DLSQAGGKEG IDGSRSGLVK KLFELIEKKE HANRPPWILI ENVPYMLRLN
RGKAMSYLTS VLSELGYTWA YRTVDARCFG LPQRRHRVIL LASLFEDPKD VIFSQDHSEP
DLDGKPSVVD HSNYYGFYWT EGLRGVGWAR EAVPPIKCGS SVGIASPPAV WSPYEDIVGT
INIRDAERLQ GFPEDWTNIT TETGKDIKEG ARWRLVGNAV SVRVSKWIGE NLSQPKGSIS
DFEGELVTKT WPSAAWGYGD KKYKVPVSKW VANTEQIAIS EFLNHPLKPL SARALNGFLG
RAARCTNVNY SDEFINSLER CKDRQLQKV
