DNMA_BACSU
ID DNMA_BACSU Reviewed; 879 AA.
AC O31504; O30579;
DT 03-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=DNA methyltransferase A {ECO:0000303|PubMed:32324221};
DE Short=DnmA {ECO:0000303|PubMed:32324221};
DE EC=2.1.1.72 {ECO:0000305|PubMed:32324221};
DE AltName: Full=Modification methylase M.Bsu3610I {ECO:0000303|PubMed:32324221};
DE AltName: Full=Modification methylase M.BsuPY79I {ECO:0000303|PubMed:32324221};
DE AltName: Full=Type II restriction enzyme and methyltransferase RM.BsuMORF6760P {ECO:0000303|PubMed:12654995};
DE Short=RM.BsuMORF6760P {ECO:0000303|PubMed:12654995};
GN Name=dnmA {ECO:0000303|PubMed:32324221}; Synonyms=yeeA;
GN OrderedLocusNames=BSU06760;
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;
RA Borriss R., Schroeter R.;
RT "The 55-58 degree segment of the Bacillus subtilis chromosome, a region
RT spanning from the purA gene cluster to the cotJ operon.";
RL Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases.
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 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 [4]
RP DNA METHYLATION, FUNCTION, DISRUPTION PHENOTYPE, DNA-BINDING, AND
RP MUTAGENESIS OF TYR-465.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501, and 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: Recognizes the double-stranded sequence 5'-GACGAG-3' and
CC methylates A-5, yielding m6A. m6A methylation functions as a
CC transcriptional modifier, promoting transcription of a number of genes
CC (at least scpA, hbs, rnhC, yumC and zapA). One studied mechanism is via
CC transcriptional repressor ScoC (also called hpr) which binds to non-
CC methylated scpA promoter; when the m6A target is methylated ScoC no
CC longer binds and scpA transcription is up-regulated. Other mechanisms
CC for gene expression regulation probably exist. Binds DNA with and
CC without the target sequence. Although it resembles a restriction-
CC modification system, it does not have detectable endonuclease activity
CC under tested conditions (PubMed:32324221). A gamma subtype methylase
CC (PubMed:12654995). {ECO:0000269|PubMed:32324221,
CC ECO:0000303|PubMed:12654995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an
CC N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:15197, Rhea:RHEA-COMP:12418, Rhea:RHEA-
CC COMP:12419, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:90615, ChEBI:CHEBI:90616; EC=2.1.1.72;
CC Evidence={ECO:0000305|PubMed:32324221};
CC -!- DISRUPTION PHENOTYPE: No visible growth defects, no A-5 methylation of
CC 5'-GACGAG-3' in strains NCIMB 3610 or PY79. Decreased promoter activity
CC for promoters with the target sequence very close to the -35 SigA-
CC binding box (scpA, hbs, rnhC, yumC and zapA).
CC {ECO:0000269|PubMed:32324221}.
CC -!- MISCELLANEOUS: Between 94.7% and 99.7% of the 5'-GACGAG-3' motifs are
CC methylated on A-5 in strain NCIMB 3610 and PY79 respectively. The sites
CC are enriched on the left chromosomal arm.
CC {ECO:0000269|PubMed:32324221}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF012532; AAB66474.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12496.1; -; Genomic_DNA.
DR PIR; E69792; E69792.
DR RefSeq; NP_388558.1; NC_000964.3.
DR RefSeq; WP_003244282.1; NZ_JNCM01000032.1.
DR AlphaFoldDB; O31504; -.
DR SMR; O31504; -.
DR STRING; 224308.BSU06760; -.
DR REBASE; 152661; Rph744ORF2800P.
DR REBASE; 152662; Rph744ORF1045P.
DR REBASE; 152669; Rph650ORF1113P.
DR REBASE; 152676; Rph620ORF1068P.
DR REBASE; 152678; Rph611ORF1113P.
DR REBASE; 152720; Rph771ORF1051P.
DR REBASE; 152725; Rph671ORF1051P.
DR REBASE; 155510; VscVS05ORF1877P.
DR REBASE; 157606; Rso10709ORF1235P.
DR REBASE; 188610; AsoACEORF469P.
DR REBASE; 191900; Apa1468ORF3364P.
DR REBASE; 22098; BsuMORF6760P.
DR REBASE; 394894; LpaCK401ORF2100P.
DR PaxDb; O31504; -.
DR PRIDE; O31504; -.
DR DNASU; 936059; -.
DR EnsemblBacteria; CAB12496; CAB12496; BSU_06760.
DR GeneID; 936059; -.
DR KEGG; bsu:BSU06760; -.
DR PATRIC; fig|224308.179.peg.734; -.
DR eggNOG; COG1002; Bacteria.
DR InParanoid; O31504; -.
DR OMA; FFAEDTD; -.
DR BioCyc; BSUB:BSU06760-MON; -.
DR PRO; PR:O31504; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IEA:RHEA.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Methyltransferase; Reference proteome; Transcription;
KW Transcription regulation; Transferase.
FT CHAIN 1..879
FT /note="DNA methyltransferase A"
FT /id="PRO_0000387939"
FT MUTAGEN 465
FT /note="Y->A: Loss of methylase activity, still binds DNA."
FT /evidence="ECO:0000269|PubMed:32324221"
FT CONFLICT 545
FT /note="Y -> N (in Ref. 1; AAB66474)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 879 AA; 101158 MW; 555B1607264285A5 CRC64;
MALIDLEDKI AEIVNREDHS DFLYELLGVY DVPRATITRL KKGNQNLTKR VGEVHLKNKV
WFKEAKKGKL FDALIDIEQQ VEYLSAKPRY LLVTDYDGVL AKDTKTLEAL DVKFEELPQY
FDFFLAWKGI EKVEFEKENP ADIKAAERFA RIYDVLRKEN NIIETNRGLD LFLIRLLFCF
FAEDTDIFKR NSFTNLIKTL TEEDGSNLNK LFADLFIVLD KNERDDVPSY LKEFPYVNGQ
LFTEPHTELE FSAKSRKLII ECGELLNWAK INPDIFGSMI QAVASEESRS YLGMHYTSVP
NIMKVIKPLF LDKLNQSFLD AYDDYTKLEN LLTRIGKIKF FDPACGSGNF LIITYKELRR
MEINIIKRLQ ELLGEYLYVP SVTLSQFYGI EIEDFAHDVA KLSLWIAEHQ MNEELKNEVH
NAVRPTLPLH TAGDIRCANA IRVEWTEVCP AQGSEEVYVF GNPPYLGSKK QNKEHKSDML
SIFGKVKNGK MLDYISAWFY FGAKYASTTN AKVAFVSTNS VTQGEQVSIL WNELFKFGIQ
INFAYKSFKW ANNAKNNAAV IVVIVGFGPL DTKVNKYLFV DETKKLVSNI SPYLTDGENI
LVSSRTKPIS DLPKLHFGNM PNDGGGLLFT ITEYTDAINK YPELVPYFKK FIGSVEFING
GLRYCLWLNE AKYEKIKSNP LIQERISISK NHREKSTDKG TNKLALTPWK FRDTHETTNY
SIVVPSVSSE NRFYIPMGLA GADTILSNLI YVIYDAEIYL LGILMSRMHM TWVKAVAGRL
KTDYRYSAGL CYNTFPIPEL STRRKNEIEE AILEILDLRE EQGGTLAELY NPSTMPIELK
VAHEKLDGIV ERAYRQKQFE SDEERLEVLL KLYQEMTER
