ID   YHDJ_ECOLI              Reviewed;         294 AA.
AC   P28638; Q2M8V3;
DT   01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-1998, sequence version 3.
DT   27-MAR-2024, entry version 165.
DE   RecName: Full=DNA adenine methyltransferase YhdJ;
DE            EC=2.1.1.72 {ECO:0000269|PubMed:17400740};
DE   AltName: Full=Type II methyltransferase M.EcoKII {ECO:0000303|PubMed:12654995};
DE            Short=M.EcoKII {ECO:0000303|PubMed:12654995};
GN   Name=yhdJ; OrderedLocusNames=b3262, JW5543;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-100.
RX   PubMed=1459953; DOI=10.1128/jb.174.24.8043-8056.1992;
RA   Ball C.A., Osuna R., Ferguson K.C., Johnson R.C.;
RT   "Dramatic changes in Fis levels upon nutrient upshift in Escherichia
RT   coli.";
RL   J. Bacteriol. 174:8043-8056(1992).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
RC   STRAIN=K12;
RX   PubMed=2835774; DOI=10.1073/pnas.85.10.3484;
RA   Johnson R.C., Ball C.A., Pfeffer D., Simon M.I.;
RT   "Isolation of the gene encoding the Hin recombinational enhancer binding
RT   protein.";
RL   Proc. Natl. Acad. Sci. U.S.A. 85:3484-3488(1988).
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, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX   PubMed=17400740; DOI=10.1128/jb.01854-06;
RA   Broadbent S.E., Balbontin R., Casadesus J., Marinus M.G., van der Woude M.;
RT   "YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli
RT   and Salmonella enterica.";
RL   J. Bacteriol. 189:4325-4327(2007).
CC   -!- FUNCTION: A beta subtype methylase, recognizes the double-stranded
CC       sequence 5'-ATGCAT-3' and methylates A-5. {ECO:0000269|PubMed:17400740,
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:0000269|PubMed:17400740};
CC   -!- DISRUPTION PHENOTYPE: Mutants are viable and show no significant growth
CC       deficiency and no alteration of cell morphology.
CC       {ECO:0000269|PubMed:17400740}.
CC   -!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA58066.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; U18997; AAA58066.1; ALT_INIT; Genomic_DNA.
DR   EMBL; U00096; AAC76294.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77303.1; -; Genomic_DNA.
DR   EMBL; M95784; AAA23784.1; -; Genomic_DNA.
DR   EMBL; J03245; AAA83857.1; -; Genomic_DNA.
DR   PIR; H65118; H65118.
DR   RefSeq; NP_417728.4; NC_000913.3.
DR   RefSeq; WP_001258895.1; NZ_SSZK01000034.1.
DR   AlphaFoldDB; P28638; -.
DR   SMR; P28638; -.
DR   BioGRID; 4262450; 211.
DR   BioGRID; 852008; 32.
DR   DIP; DIP-12296N; -.
DR   IntAct; P28638; 34.
DR   STRING; 511145.b3262; -.
DR   REBASE; 13375; M.EcoW3110ORF3249P.
DR   REBASE; 191860; M.Apa1447ORF405P.
DR   REBASE; 191899; M.Apa1342ORF402P.
DR   REBASE; 191903; M.Apa1468ORF401P.
DR   REBASE; 232308; M.Sen4024ORF451P.
DR   REBASE; 232685; M.Sen4839ORF451P.
DR   REBASE; 3885; M.EcoKII.
DR   REBASE; 400747; M.Eco6192ORF11P.
DR   REBASE; 441486; M.EcoBL21FORF3183P.
DR   REBASE; 701539; M.EcoKORFAP.
DR   REBASE; 757850; M.Eco320ORF8P.
DR   PaxDb; 511145-b3262; -.
DR   EnsemblBacteria; AAC76294; AAC76294; b3262.
DR   GeneID; 947695; -.
DR   KEGG; ecj:JW5543; -.
DR   KEGG; eco:b3262; -.
DR   PATRIC; fig|511145.12.peg.3361; -.
DR   EchoBASE; EB1461; -.
DR   eggNOG; COG2189; Bacteria.
DR   HOGENOM; CLU_024927_5_2_6; -.
DR   InParanoid; P28638; -.
DR   OMA; SIHKMSA; -.
DR   OrthoDB; 9816043at2; -.
DR   PhylomeDB; P28638; -.
DR   BioCyc; EcoCyc:EG11498-MONOMER; -.
DR   BioCyc; MetaCyc:EG11498-MONOMER; -.
DR   PRO; PR:P28638; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0008170; F:N-methyltransferase activity; IEA:InterPro.
DR   GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IDA:EcoCyc.
DR   CDD; cd02440; AdoMet_MTases; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR   InterPro; IPR002941; DNA_methylase_N4/N6.
DR   InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR   InterPro; IPR001091; RM_Methyltransferase.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   PANTHER; PTHR13370:SF32; DNA ADENINE METHYLTRANSFERASE YHDJ; 1.
DR   PANTHER; PTHR13370; RNA METHYLASE-RELATED; 1.
DR   Pfam; PF01555; N6_N4_Mtase; 1.
DR   PRINTS; PR00508; S21N4MTFRASE.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS00092; N6_MTASE; 1.
PE   1: Evidence at protein level;
KW   DNA-binding; Methyltransferase; Reference proteome;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..294
FT                   /note="DNA adenine methyltransferase YhdJ"
FT                   /id="PRO_0000088000"
FT   REGION          275..294
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        28
FT                   /note="K -> N (in Ref. 3; AAA23784)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   294 AA;  33397 MW;  6BCC49D9A571884B CRC64;
     MRTGCEPTRF GNEAKTIIHG DALAELKKIP AESVDLIFAD PPYNIGKNFD GLIEAWKEDL
     FIDWLFEVIA ECHRVLKKQG SMYIMNSTEN MPFIDLQCRK LFTIKSRIVW SYDSSGVQAK
     KHYGSMYEPI LMMVKDAKNY TFNGDAILVE AKTGSQRALI DYRKNPPQPY NHQKVPGNVW
     DFPRVRYLMD EYENHPTQKP EALLKRIILA SSNPGDIVLD PFAGSFTTGA VAIASGRKFI
     GIEINSEYIK MGLRRLDVAS HYSAEELAKV KKRKTGNLSK RSRLSEVDPD LITK
//