TRM4A_SCHPO
ID TRM4A_SCHPO Reviewed; 688 AA.
AC Q9HGQ2; Q9P3W7;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2012, sequence version 3.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Multisite-specific tRNA:(cytosine-C(5))-methyltransferase trm4a {ECO:0000305};
DE EC=2.1.1.- {ECO:0000305|PubMed:23074192, ECO:0000305|PubMed:30646830};
DE EC=2.1.1.203 {ECO:0000305|PubMed:30646830};
DE AltName: Full=tRNA (cytosine-5-)-methyltransferase trm4a;
GN Name=trm4a {ECO:0000303|PubMed:30646830, ECO:0000312|PomBase:SPAC17D4.04};
GN ORFNames=SPAC17D4.04, SPAC458.01;
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-54, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=18257517; DOI=10.1021/pr7006335;
RA Wilson-Grady J.T., Villen J., Gygi S.P.;
RT "Phosphoproteome analysis of fission yeast.";
RL J. Proteome Res. 7:1088-1097(2008).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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 [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND CATALYTIC ACTIVITY.
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 34 and 48
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(48) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(48) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:54136, Rhea:RHEA-COMP:13806, Rhea:RHEA-
CC COMP:13807, 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:54137;
CC Evidence={ECO:0000269|PubMed:23074192, ECO:0000269|PubMed:30646830};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(34) in tRNA precursor + S-adenosyl-L-methionine = 5-
CC methylcytidine(34) in tRNA precursor + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42940, Rhea:RHEA-COMP:10291, Rhea:RHEA-
CC COMP:10295, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.203;
CC Evidence={ECO:0000305|PubMed:30646830};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42941;
CC Evidence={ECO:0000269|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}. Cytoplasm
CC {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; CAC05734.3; -; Genomic_DNA.
DR RefSeq; NP_594695.3; NM_001020123.2.
DR AlphaFoldDB; Q9HGQ2; -.
DR SMR; Q9HGQ2; -.
DR BioGRID; 278733; 2.
DR STRING; 4896.SPAC17D4.04.1; -.
DR iPTMnet; Q9HGQ2; -.
DR MaxQB; Q9HGQ2; -.
DR PaxDb; Q9HGQ2; -.
DR PRIDE; Q9HGQ2; -.
DR EnsemblFungi; SPAC17D4.04.1; SPAC17D4.04.1:pep; SPAC17D4.04.
DR GeneID; 2542264; -.
DR KEGG; spo:SPAC17D4.04; -.
DR PomBase; SPAC17D4.04; -.
DR VEuPathDB; FungiDB:SPAC17D4.04; -.
DR eggNOG; KOG2198; Eukaryota.
DR HOGENOM; CLU_005316_4_3_1; -.
DR InParanoid; Q9HGQ2; -.
DR OMA; WRRWNAG; -.
DR BRENDA; 2.1.1.202; 5613.
DR PRO; PR:Q9HGQ2; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
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:0002946; P:tRNA C5-cytosine methylation; IC:PomBase.
DR GO; GO:0030488; P:tRNA methylation; IMP:UniProtKB.
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 Cytoplasm; Methyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; S-adenosyl-L-methionine; Transferase; tRNA processing;
KW tRNA-binding.
FT CHAIN 1..688
FT /note="Multisite-specific tRNA:(cytosine-C(5))-
FT methyltransferase trm4a"
FT /id="PRO_0000211824"
FT REGION 439..474
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 309
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 203
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 230
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 256
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT MOD_RES 54
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:18257517"
SQ SEQUENCE 688 AA; 78515 MW; 30663979A4592269 CRC64;
MGRKHYSSKK NRSKKGEFVN WDLIERKNEN FEKYYRLQKL VTEDDFILLK QKLTEQLPTT
FRITASIPHA TQVRDYFIEH YYPLIENART EDAKIPLPVS LPWYPDGMAF MLDISKEVIR
KSPHLKALQE FLVLETEAGD INRQESVSMV PPLLLNVESH HKVLDMCAAP GSKTAQLLEA
LHKPTKKEDI TTLLPSGIVI ANDSDNKRAH MLVHQIKRLN SPNVLIVNHD ASFLPNFHLS
SPDGKKFLKF DRILADVPCS GDGTFRKNIA LWNEWSLKTA LGLHATQIKI LMRGLQLLEK
GGRLVYSTCS LNPIENEAVV SAVLNATRGS VRLVDVSSEL PQLKRSQGVD NWVVCDSDLN
IYPSFDTLPK ELYEKMPPTL WPLPKKELAE LNIQNCLRIY PHFQNTGGFF VAVLEKYENL
TSSMKTAVDD NKVFLREQKL PSEQASKKRK QDTQETSSDS KLAEVKPKGK NGGNRFHELD
PFVYIKEDDQ ALEKIYKKFG IDEAIIKKNQ FFVRNVNGVP TKAIYISNDL FRNVIENNRN
RVKFVHGGLK IFVRQDFGSL SREIAEKNGT CVFRVQSDGA NLASHFIAES CLFHTTLSDL
FILLDHEAVT IDDFPEDSLF RKEYNHLDLG STLLHVDLAK EESVIKKQVY IPLWKSVRIC
NVLLSNSEKR TLKLQIEGPQ SSIHKHNT
