PMT1M_SCHPO
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 03-AUG-2022, entry version 139.
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; 4896.SPBC19C2.02.1; -.
DR MaxQB; P40999; -.
DR PaxDb; P40999; -.
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; VMDIIHP; -.
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 (cytosine) methyltransferase activity; IDA:PomBase.
DR GO; GO:0016428; F:tRNA (cytosine-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 DisProt; DP02685; -.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR031303; C5_meth_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 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
