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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
 
 
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