TRM2_YEAST
ID TRM2_YEAST Reviewed; 639 AA.
AC P33753; D6VXB7; P30618; Q86ZR6; Q9HGQ5;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 25-JUL-2006, sequence version 2.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=tRNA (uracil(54)-C(5))-methyltransferase;
DE EC=2.1.1.35;
DE AltName: Full=Transfer RNA methyltransferase 2;
DE AltName: Full=tRNA(m5U54)-methyltransferase;
GN Name=TRM2; Synonyms=NUC2, NUD1, RNC1; OrderedLocusNames=YKR056W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8256523; DOI=10.1002/yea.320091015;
RA van Vliet-Reedijk J.C., Planta R.J.;
RT "The RHO4a and NUD1 genes on Saccharomyces cerevisiae chromosome XI.";
RL Yeast 9:1139-1147(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION OF FRAMESHIFT, FUNCTION,
RP AND CATALYTIC ACTIVITY.
RX PubMed=10864043; DOI=10.1017/s1355838200992422;
RA Nordlund M.E., Johansson J.O.M., Von Pawel-Rammingen U., Bystroem A.S.;
RT "Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase
RT of Saccharomyces cerevisiae.";
RL RNA 6:844-860(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8196765; DOI=10.1038/369371a0;
RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA Becker I., Mewes H.-W.;
RT "Complete DNA sequence of yeast chromosome XI.";
RL Nature 369:371-378(1994).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-168.
RX PubMed=1408836; DOI=10.1093/nar/20.19.5215;
RA Chow T.Y.-K., Perkins E.L., Resnick M.A.;
RT "Yeast RNC1 encodes a chimeric protein, RhoNUC, with a human rho motif and
RT deoxyribonuclease activity.";
RL Nucleic Acids Res. 20:5215-5221(1992).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 552-628, AND IDENTIFICATION OF
RP FRAMESHIFT.
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=12844361; DOI=10.1186/gb-2003-4-7-r45;
RA Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A.,
RA Gates K., Gaffney T.D., Philippsen P.;
RT "Reinvestigation of the Saccharomyces cerevisiae genome annotation by
RT comparison to the genome of a related fungus: Ashbya gossypii.";
RL Genome Biol. 4:R45.1-R45.13(2003).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF GLY-498 AND CYS-591.
RX PubMed=12003492; DOI=10.1017/s1355838202027851;
RA Johansson M.J., Bystroem A.S.;
RT "Dual function of the tRNA(m(5)U54)methyltransferase in tRNA maturation.";
RL RNA 8:324-335(2002).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-92 AND SER-93, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-92 AND SER-93, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 54
CC (m5U54) in all tRNA. May also have a role in tRNA stabilization or
CC maturation. {ECO:0000269|PubMed:10864043, ECO:0000269|PubMed:12003492}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(54) in tRNA = 5-
CC methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42712, Rhea:RHEA-COMP:10167, Rhea:RHEA-COMP:10193,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.35;
CC Evidence={ECO:0000269|PubMed:10864043};
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01024}.
CC -!- CAUTION: Was originally thought to be an endo-exonuclease.
CC {ECO:0000305|PubMed:1408836}.
CC -!- CAUTION: It is uncertain whether Met-1, Met-38, Met-71, Met-77 or Met-
CC 82 is the initiator. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA78500.1; Type=Miscellaneous discrepancy; Note=Cloning artifact which fused this protein with RHO4.; Evidence={ECO:0000305};
CC Sequence=CAA81021.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA82134.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAC01942.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; Z25734; CAA81021.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AJ250970; CAC01942.1; ALT_INIT; Genomic_DNA.
DR EMBL; Z28281; CAA82134.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Z14126; CAA78500.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AY260897; AAP21765.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09207.1; -; Genomic_DNA.
DR PIR; S37744; S37744.
DR RefSeq; NP_012982.2; NM_001179846.1.
DR AlphaFoldDB; P33753; -.
DR SMR; P33753; -.
DR BioGRID; 34187; 106.
DR MINT; P33753; -.
DR STRING; 4932.YKR056W; -.
DR iPTMnet; P33753; -.
DR MaxQB; P33753; -.
DR PaxDb; P33753; -.
DR PRIDE; P33753; -.
DR EnsemblFungi; YKR056W_mRNA; YKR056W; YKR056W.
DR GeneID; 853930; -.
DR KEGG; sce:YKR056W; -.
DR SGD; S000001764; TRM2.
DR VEuPathDB; FungiDB:YKR056W; -.
DR eggNOG; KOG2187; Eukaryota.
DR GeneTree; ENSGT00530000063723; -.
DR HOGENOM; CLU_014689_3_2_1; -.
DR InParanoid; P33753; -.
DR OMA; FYAGDMK; -.
DR BioCyc; YEAST:G3O-32025-MON; -.
DR PRO; PR:P33753; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P33753; protein.
DR GO; GO:0051908; F:double-stranded DNA 5'-3' exodeoxyribonuclease activity; IDA:SGD.
DR GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IDA:SGD.
DR GO; GO:0030696; F:tRNA (m5U54) methyltransferase activity; IDA:SGD.
DR GO; GO:0006400; P:tRNA modification; IDA:SGD.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR002792; TRAM_dom.
DR InterPro; IPR025795; tRNA_(uracil-5-)_MeTrfase.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS50926; TRAM; 1.
DR PROSITE; PS01230; TRMA_1; 1.
DR PROSITE; PS01231; TRMA_2; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Phosphoprotein; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..639
FT /note="tRNA (uracil(54)-C(5))-methyltransferase"
FT /id="PRO_0000162059"
FT DOMAIN 163..228
FT /note="TRAM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00208"
FT REGION 78..113
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 78..99
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 591
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT ACT_SITE 631
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10015"
FT BINDING 461
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 496
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 517
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 564
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT MOD_RES 92
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 93
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MUTAGEN 498
FT /note="G->D: Unable to methylate tRNA."
FT /evidence="ECO:0000269|PubMed:12003492"
FT MUTAGEN 591
FT /note="C->A: Unable to methylate tRNA."
FT /evidence="ECO:0000269|PubMed:12003492"
FT CONFLICT 24
FT /note="H -> Y (in Ref. 5; CAA78500)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 639 AA; 72852 MW; E7EC5B1378F7C361 CRC64;
MYEQFEFSFF FFENSDNKVK YKAHLISSIK RWSIITCMRC FWTVQKSIFK ARFFACRNFV
KKHNYKLIST MTGSTEMVPP TMKHTVDNKR LSSPLTDSGN RRTKKPKLRK YKAKKVETTS
PMGVLEFEVN DLLKSQNLSR EQVLNDVTSI LNDKSSTDGP IVLQYHREVK NVKVLEITSN
GNGLALIDNP VETEKKQVVI IPFGLPGDVV NIKVFKTHPY YVESDLLDVV EKSPMRRDDL
IRDKYFGKSS GSQLEFLTYD DQLELKRKTI MNAYKFFAPR LVAEKLLPPF DTTVASPLQF
GYRTKITPHF DMPKRKQKEL SVRPPLGFGQ KGRPQWRKDT LDIGGHGSIL DIDECVLATE
VLNKGLTNER RKFEQEFKNY KKGATILLRE NTTILDPSKP TLEQLTEEAS RDENGDISYV
EVEDKKNNVR LAKTCVTNPR QIVTEYVDGY TFNFSAGEFF QNNNSILPIV TKYVRDNLQA
PAKGDDNKTK FLVDAYCGSG LFSICSSKGV DKVIGVEISA DSVSFAEKNA KANGVENCRF
IVGKAEKLFE SIDTPSENTS VILDPPRKGC DELFLKQLAA YNPAKIIYIS CNVHSQARDV
EYFLKETENG SAHQIESIRG FDFFPQTHHV ESVCIMKRI
