TRM4B_SCHPO
ID TRM4B_SCHPO Reviewed; 685 AA.
AC O13935;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2012, sequence version 2.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Multisite-specific tRNA:(cytosine-C(5))-methyltransferase trm4b;
DE EC=2.1.1.- {ECO:0000305|PubMed:23074192, ECO:0000305|PubMed:30646830};
DE AltName: Full=tRNA (cytosine-5-)-methyltransferase trm4b;
GN Name=trm4b {ECO:0000303|PubMed:30646830, ECO:0000312|PomBase:SPAC23C4.17};
GN ORFNames=SPAC23C4.17;
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 [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 [2]
RP REVISION OF GENE MODEL.
RX PubMed=21511999; DOI=10.1126/science.1203357;
RA Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N.,
RA Wapinski I., Roy S., Lin M.F., Heiman D.I., Young S.K., Furuya K., Guo Y.,
RA Pidoux A., Chen H.M., Robbertse B., Goldberg J.M., Aoki K., Bayne E.H.,
RA Berlin A.M., Desjardins C.A., Dobbs E., Dukaj L., Fan L., FitzGerald M.G.,
RA French C., Gujja S., Hansen K., Keifenheim D., Levin J.Z., Mosher R.A.,
RA Mueller C.A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P.,
RA Sykes S.M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R.,
RA Baulcombe D., Birren B.W., Brown W., Ekwall K., Kellis M., Leatherwood J.,
RA Levin H., Margalit H., Martienssen R., Nieduszynski C.A., Spatafora J.W.,
RA Friedman N., Dalgaard J.Z., Baumann P., Niki H., Regev A., Nusbaum C.;
RT "Comparative functional genomics of the fission yeasts.";
RL Science 332:930-936(2011).
RN [3]
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 [4]
RP FUNCTION.
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).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=30646830; DOI=10.1080/15476286.2019.1568819;
RA Mueller M., Samel-Pommerencke A., Legrand C., Tuorto F., Lyko F.,
RA Ehrenhofer-Murray A.E.;
RT "Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases
RT Trm4a and Trm4b in fission yeast.";
RL RNA Biol. 16:249-256(2019).
CC -!- FUNCTION: tRNA cytosine C(5)-methyltransferase that methylates cytosine
CC to 5-methylcytosine (m5C) in tRNAs at position 49 and 50
CC (PubMed:30646830). Trm4a and trm4b methylate different sets of tRNAs
CC (PubMed:30646830). Also methylates cytosine to m5C at positions (60, 61
CC and 62) in tRNA(Asp) (PubMed:23074192). {ECO:0000269|PubMed:23074192,
CC ECO:0000269|PubMed:30646830}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(49) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(49) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:54140, Rhea:RHEA-COMP:13804, Rhea:RHEA-
CC COMP:13805, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:23074192, ECO:0000305|PubMed:30646830};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:54141;
CC Evidence={ECO:0000269|PubMed:23074192, ECO:0000305|PubMed:30646830};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(50) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(50) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61488, Rhea:RHEA-COMP:15838, Rhea:RHEA-COMP:15839,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:30646830};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61489;
CC Evidence={ECO:0000305|PubMed:30646830};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(60) in tRNA(Asp) + S-adenosyl-L-methionine = 5-
CC methylcytidine(60) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:51160, Rhea:RHEA-COMP:12902, Rhea:RHEA-COMP:12905,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:23074192};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:51161;
CC Evidence={ECO:0000269|PubMed:23074192};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(61) in tRNA(Asp) + S-adenosyl-L-methionine = 5-
CC methylcytidine(61) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:51164, Rhea:RHEA-COMP:12903, Rhea:RHEA-COMP:12906,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:23074192};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:51165;
CC Evidence={ECO:0000269|PubMed:23074192};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(62) in tRNA(Asp) + S-adenosyl-L-methionine = 5-
CC methylcytidine(62) in tRNA(Asp) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:51172, Rhea:RHEA-COMP:12904, Rhea:RHEA-COMP:12907,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000305|PubMed:23074192};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:51173;
CC Evidence={ECO:0000269|PubMed:23074192};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16823372}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking both trm4a and trm4b show a mild
CC resistance to calcium chloride. {ECO:0000269|PubMed:30646830}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. TRM4 subfamily. {ECO:0000255|PROSITE-
CC ProRule:PRU01023}.
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DR EMBL; CU329670; CAB16888.2; -; Genomic_DNA.
DR PIR; T38272; T38272.
DR RefSeq; NP_593189.2; NM_001018585.2.
DR AlphaFoldDB; O13935; -.
DR SMR; O13935; -.
DR BioGRID; 278407; 2.
DR STRING; 4896.SPAC23C4.17.1; -.
DR MaxQB; O13935; -.
DR PaxDb; O13935; -.
DR PRIDE; O13935; -.
DR EnsemblFungi; SPAC23C4.17.1; SPAC23C4.17.1:pep; SPAC23C4.17.
DR GeneID; 2541917; -.
DR KEGG; spo:SPAC23C4.17; -.
DR PomBase; SPAC23C4.17; -.
DR VEuPathDB; FungiDB:SPAC23C4.17; -.
DR eggNOG; KOG2198; Eukaryota.
DR HOGENOM; CLU_005316_4_3_1; -.
DR InParanoid; O13935; -.
DR OMA; KSLWPQG; -.
DR BRENDA; 2.1.1.202; 5613.
DR PRO; PR:O13935; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0008168; F:methyltransferase activity; IBA:GO_Central.
DR GO; GO:0062152; F:mRNA (cytidine-5-)-methyltransferase activity; ISS:PomBase.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IMP:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IMP:UniProtKB.
DR GO; GO:0002127; P:tRNA wobble base cytosine methylation; ISO:PomBase.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR023270; RCMT_NCL1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22808; PTHR22808; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR PRINTS; PR02011; RCMTNCL1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Reference proteome; RNA-binding;
KW S-adenosyl-L-methionine; Transferase; tRNA processing; tRNA-binding.
FT CHAIN 1..685
FT /note="Multisite-specific tRNA:(cytosine-C(5))-
FT methyltransferase trm4b"
FT /id="PRO_0000317151"
FT ACT_SITE 323
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 167..173
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 208
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 235
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 270
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
SQ SEQUENCE 685 AA; 77822 MW; 824E4D2ACB8B1C5A CRC64;
MGKRNKKVTQ GKRAYNDKSE IVLENKQFEG YYKKQNLFRG KPNDEFDSFM EYMRKPLPTT
FRICGYRHHA FELKNHFEKY YVPSLKNVVH EGQTIPPPTV LPWYPDGLAY IVDAQKDVIR
KSPPLKRLQR FLVSENEAGN INRQEAVSML PPLFLDVEPH HVILDMCAAP GSKTAQLIEA
VYKKANIKDA AHDSKNLKSV EGLVIANDAD PKRAQMLVHQ INRLNSPNIL VVNHDASTMP
NIYVKGSSPS DGLNVIEEKK ILKFDRILAD VPCSGDGTFR KNLSLWREWS ANSAFSLHPL
QLRILIRGLQ LLKVGGCLVY STCSINPIEN EAVVTAALKA TGGAVSLVDV SKKLPLLKRD
PGLLSWKVLD DSLNEFQSPA ENTNDKIELT ESMWPLPEEE MSKLHIERCA RLYPHMQNTG
GFFVAVLQKT DPINSRSFDP KKYTASMEIL PPENKRQRTE KGVDEASNST LTKSGNSYFD
EEPFVYINPD DTSIKTIVDF YGIDPSFPRD QFFVRNQSGI PVRSIYFACS LFKEIIEANT
NRVKFVHGGV RFFVKQEISQ LLKDFSLKAN KDICNFRIHS NGVNIISPFL NEKHFYDAGL
KDLKILVKNE YPHVEQFSES GMLKKEFEKM PLGCNILRVD AQTKDGALMD MLILQPIWRS
PTSCNLMLAR KEKQNLSLEL FGMDV
