ID   PMT1M_SCHPO             Reviewed;         330 AA.
AC   P40999;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 1.
DT   24-JAN-2024, entry version 145.
DE   RecName: Full=tRNA (cytosine(38)-C(5))-methyltransferase;
DE            EC=2.1.1.204;
DE   AltName: Full=DNA (cytosine-5)-methyltransferase-like protein 2;
DE            Short=Dnmt2;
DE   AltName: Full=M.SpomI;
DE   AltName: Full=SpIM.SpoI;
GN   Name=pmt1; ORFNames=SPBC19C2.02;
OS   Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC   Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC   Schizosaccharomyces.
OX   NCBI_TaxID=284812;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC   STRAIN=972 / ATCC 24843;
RX   PubMed=7862522; DOI=10.1093/nar/23.2.203;
RA   Wilkinson C.R.M., Bartlett R., Nurse P., Bird A.P.;
RT   "The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.";
RL   Nucleic Acids Res. 23:203-210(1995).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=972 / ATCC 24843;
RX   PubMed=11859360; DOI=10.1038/nature724;
RA   Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA   Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA   Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA   Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA   Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA   Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA   Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA   Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA   O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA   Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA   Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA   Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA   Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA   Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA   Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA   Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA   Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA   Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA   Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA   Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA   del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA   Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA   Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA   Nurse P.;
RT   "The genome sequence of Schizosaccharomyces pombe.";
RL   Nature 415:871-880(2002).
RN   [3]
RP   CHARACTERIZATION.
RX   PubMed=8636983; DOI=10.1006/jmbi.1996.0203;
RA   Pinarbasi E., Elliott J., Hornby D.P.;
RT   "Activation of a yeast pseudo DNA methyltransferase by deletion of a single
RT   amino acid.";
RL   J. Mol. Biol. 257:804-813(1996).
RN   [4]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=16823372; DOI=10.1038/nbt1222;
RA   Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA   Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA   Yoshida M.;
RT   "ORFeome cloning and global analysis of protein localization in the fission
RT   yeast Schizosaccharomyces pombe.";
RL   Nat. Biotechnol. 24:841-847(2006).
RN   [5]
RP   FUNCTION, MUTAGENESIS OF CYS-81, AND INDUCTION.
RX   PubMed=23074192; DOI=10.1093/nar/gks956;
RA   Becker M., Muller S., Nellen W., Jurkowski T.P., Jeltsch A.,
RA   Ehrenhofer-Murray A.E.;
RT   "Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA
RT   methylation in response to nutrient signaling.";
RL   Nucleic Acids Res. 40:11648-11658(2012).
CC   -!- FUNCTION: Specifically methylates cytosine 38 in the anticodon loop of
CC       tRNA(Asp). Can also methylate cytosine 38 in tRNA(Glu), albeit to a
CC       lower level, but not tRNA(Lys). Pmt1-dependent tRNA methylation is
CC       induced by nitrogen limitation and depends on the nutrient-sensing
CC       protein kinase sck2. Does not have DNA-methylation activity.
CC       {ECO:0000269|PubMed:23074192}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=cytidine(38) in tRNA + S-adenosyl-L-methionine = 5-
CC         methylcytidine(38) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:42956, Rhea:RHEA-COMP:10299, Rhea:RHEA-COMP:10300,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.204;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16823372}. Nucleus
CC       {ECO:0000269|PubMed:16823372}.
CC   -!- INDUCTION: Constitutively expressed at protein and RNA levels.
CC       {ECO:0000269|PubMed:23074192}.
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC       ProRule:PRU01016}.
CC   -!- CAUTION: Was originally thought not to have cytosine-5
CC       methyltransferase activity, and this was attributed to the insertion of
CC       a Ser residue between the Pro-Cys motif found at the active site of C5
CC       MTases (PubMed:8636983). When this serine is deleted it becomes
CC       catalytically active and recognizes and methylates the sequence
CC       CC[AT]GG. This was in agreement with S.pombe lacking m5C DNA-
CC       methylation. However, it has later been shown that it has tRNA-
CC       methyltransferase activity despite this sequence variation
CC       (PubMed:23074192). {ECO:0000305|PubMed:23074192,
CC       ECO:0000305|PubMed:8636983}.
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DR   EMBL; X82444; CAA57824.1; -; Genomic_DNA.
DR   EMBL; CU329671; CAB52029.1; -; Genomic_DNA.
DR   PIR; S53990; S53990.
DR   RefSeq; NP_595687.1; NM_001021584.2.
DR   PDB; 6FDF; X-ray; 1.70 A; A/B/C/D=2-330.
DR   PDBsum; 6FDF; -.
DR   AlphaFoldDB; P40999; -.
DR   SMR; P40999; -.
DR   BioGRID; 277286; 17.
DR   STRING; 284812.P40999; -.
DR   MaxQB; P40999; -.
DR   PaxDb; 4896-SPBC19C2-02-1; -.
DR   EnsemblFungi; SPBC19C2.02.1; SPBC19C2.02.1:pep; SPBC19C2.02.
DR   GeneID; 2540766; -.
DR   KEGG; spo:SPBC19C2.02; -.
DR   PomBase; SPBC19C2.02; pmt1.
DR   VEuPathDB; FungiDB:SPBC19C2.02; -.
DR   eggNOG; KOG0919; Eukaryota.
DR   HOGENOM; CLU_049101_0_0_1; -.
DR   InParanoid; P40999; -.
DR   OMA; HYAFKYA; -.
DR   PhylomeDB; P40999; -.
DR   BRENDA; 2.1.1.203; 5613.
DR   BRENDA; 2.1.1.204; 5613.
DR   PRO; PR:P40999; -.
DR   Proteomes; UP000002485; Chromosome II.
DR   GO; GO:0005829; C:cytosol; HDA:PomBase.
DR   GO; GO:0005634; C:nucleus; HDA:PomBase.
DR   GO; GO:0016427; F:tRNA (cytidine) methyltransferase activity; IDA:PomBase.
DR   GO; GO:0016428; F:tRNA (cytidine-5-)-methyltransferase activity; IDA:PomBase.
DR   GO; GO:0000049; F:tRNA binding; IC:PomBase.
DR   GO; GO:0002946; P:tRNA C5-cytosine methylation; IMP:PomBase.
DR   CDD; cd00315; Cyt_C5_DNA_methylase; 1.
DR   DisProt; DP02685; -.
DR   Gene3D; 3.90.120.10; DNA Methylase, subunit A, domain 2; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR   InterPro; IPR001525; C5_MeTfrase.
DR   InterPro; IPR031303; C5_meth_CS.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   NCBIfam; TIGR00675; dcm; 1.
DR   PANTHER; PTHR46098; TRNA (CYTOSINE(38)-C(5))-METHYLTRANSFERASE; 1.
DR   PANTHER; PTHR46098:SF1; TRNA (CYTOSINE(38)-C(5))-METHYLTRANSFERASE; 1.
DR   Pfam; PF00145; DNA_methylase; 1.
DR   PRINTS; PR00105; C5METTRFRASE.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS00095; C5_MTASE_2; 1.
DR   PROSITE; PS51679; SAM_MT_C5; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Methyltransferase; Nucleus; Reference proteome;
KW   RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT   CHAIN           1..330
FT                   /note="tRNA (cytosine(38)-C(5))-methyltransferase"
FT                   /id="PRO_0000088042"
FT   DOMAIN          7..330
FT                   /note="SAM-dependent MTase C5-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT   ACT_SITE        81
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT   MUTAGEN         81
FT                   /note="C->A: Loss of methyltransferase activity."
FT                   /evidence="ECO:0000269|PubMed:23074192"
FT   STRAND          7..13
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   TURN            15..17
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           18..25
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          30..38
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           40..50
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          54..56
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           59..61
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           64..70
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          73..77
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          83..85
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           99..107
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           108..110
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          111..113
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          116..123
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           126..128
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           130..141
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          144..151
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           153..155
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          164..171
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           179..185
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          192..195
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           198..200
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           209..211
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           215..221
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           222..224
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   TURN            240..244
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   STRAND          252..254
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           261..268
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           269..272
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           279..285
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           301..309
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           314..324
FT                   /evidence="ECO:0007829|PDB:6FDF"
FT   HELIX           326..328
FT                   /evidence="ECO:0007829|PDB:6FDF"
SQ   SEQUENCE   330 AA;  37976 MW;  50A7121FA7CF58A1 CRC64;
     MLSTKRLRVL ELYSGIGGMH YALNLANIPA DIVCAIDINP QANEIYNLNH GKLAKHMDIS
     TLTAKDFDAF DCKLWTMSPS CQPFTRIGNR KDILDPRSQA FLNILNVLPH VNNLPEYILI
     ENVQGFEESK AAEECRKVLR NCGYNLIEGI LSPNQFNIPN SRSRWYGLAR LNFKGEWSID
     DVFQFSEVAQ KEGEVKRIRD YLEIERDWSS YMVLESVLNK WGHQFDIVKP DSSSCCCFTR
     GYTHLVQGAG SILQMSDHEN THEQFERNRM ALQLRYFTAR EVARLMGFPE SLEWSKSNVT
     EKCMYRLLGN SINVKVVSYL ISLLLEPLNF
//