TRMB_YEAST
ID TRMB_YEAST Reviewed; 286 AA.
AC Q12009; D6VRF3;
DT 20-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=tRNA (guanine-N(7)-)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_03055};
DE EC=2.1.1.33 {ECO:0000255|HAMAP-Rule:MF_03055};
DE AltName: Full=Transfer RNA methyltransferase 8 {ECO:0000255|HAMAP-Rule:MF_03055};
DE AltName: Full=tRNA (guanine(46)-N(7))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_03055};
DE AltName: Full=tRNA(m7G46)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_03055};
GN Name=TRM8 {ECO:0000255|HAMAP-Rule:MF_03055}; OrderedLocusNames=YDL201W;
GN ORFNames=D1075;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
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 [3]
RP CHARACTERIZATION, AND INTERACTION WITH TRM82.
RX PubMed=12403464; DOI=10.1017/s1355838202024019;
RA Alexandrov A., Martzen M.R., Phizicky E.M.;
RT "Two proteins that form a complex are required for 7-methylguanosine
RT modification of yeast tRNA.";
RL RNA 8:1253-1266(2002).
RN [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [5]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [6]
RP CATALYTIC ACTIVITY, TRNA-BINDING, AND INTERACTION WITH TRM82.
RX PubMed=15811913; DOI=10.1261/rna.2030705;
RA Alexandrov A., Grayhack E.J., Phizicky E.M.;
RT "tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a
RT growth phenotype and implicating Trm82p in maintaining levels of active
RT Trm8p.";
RL RNA 11:821-830(2005).
RN [7]
RP FUNCTION.
RX PubMed=16387656; DOI=10.1016/j.molcel.2005.10.036;
RA Alexandrov A., Chernyakov I., Gu W., Hiley S.L., Hughes T.R.,
RA Grayhack E.J., Phizicky E.M.;
RT "Rapid tRNA decay can result from lack of nonessential modifications.";
RL Mol. Cell 21:87-96(2006).
RN [8]
RP FUNCTION.
RX PubMed=17382321; DOI=10.1016/j.febslet.2007.03.023;
RA Matsumoto K., Toyooka T., Tomikawa C., Ochi A., Takano Y., Takayanagi N.,
RA Endo Y., Hori H.;
RT "RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase
RT (Trm8-Trm82 complex).";
RL FEBS Lett. 581:1599-1604(2007).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59, AND IDENTIFICATION BY
RP 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, AND IDENTIFICATION BY MASS
RP 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-59, AND IDENTIFICATION BY
RP 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).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 29-286 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE AND TRM82, SUBUNIT, AND PROBABLE ACTIVE SITE.
RX PubMed=18184583; DOI=10.1016/j.str.2007.10.025;
RA Leulliot N., Chaillet M., Durand D., Ulryck N., Blondeau K.,
RA van Tilbeurgh H.;
RT "Structure of the yeast tRNA m7G methylation complex.";
RL Structure 16:52-61(2008).
CC -!- FUNCTION: Methyltransferase that catalyzes the formation of N(7)-
CC methylguanine at position 46 (m7G46) in tRNA, a modification required
CC to maintain stability of tRNAs; its absence resulting in tRNA decay.
CC Both the D-stem and T-stem structures of tRNAs are required for
CC efficient methyltransferase activity. {ECO:0000255|HAMAP-Rule:MF_03055,
CC ECO:0000269|PubMed:16387656, ECO:0000269|PubMed:17382321}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(46) in tRNA + S-adenosyl-L-methionine = N(7)-
CC methylguanosine(46) in tRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42708, Rhea:RHEA-COMP:10188, Rhea:RHEA-COMP:10189,
CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74269,
CC ChEBI:CHEBI:74480; EC=2.1.1.33; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03055, ECO:0000269|PubMed:15811913};
CC -!- PATHWAY: tRNA modification; N(7)-methylguanine-tRNA biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_03055}.
CC -!- SUBUNIT: Forms a complex with TRM82. {ECO:0000255|HAMAP-Rule:MF_03055,
CC ECO:0000269|PubMed:18184583}.
CC -!- INTERACTION:
CC Q12009; Q03774: TRM82; NbExp=8; IntAct=EBI-19552, EBI-19486;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03055,
CC ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 2630 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. TrmB family. {ECO:0000255|HAMAP-Rule:MF_03055}.
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DR EMBL; X99000; CAA67468.1; -; Genomic_DNA.
DR EMBL; Z74249; CAA98779.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11663.1; -; Genomic_DNA.
DR PIR; S67760; S67760.
DR RefSeq; NP_010080.1; NM_001180261.1.
DR PDB; 2VDU; X-ray; 2.40 A; E/F=39-286.
DR PDB; 2VDV; X-ray; 2.30 A; E/F=47-286.
DR PDBsum; 2VDU; -.
DR PDBsum; 2VDV; -.
DR AlphaFoldDB; Q12009; -.
DR SMR; Q12009; -.
DR BioGRID; 31845; 79.
DR ComplexPortal; CPX-1632; tRNA (guanine-N(7)-)-methyltransferase.
DR DIP; DIP-8614N; -.
DR IntAct; Q12009; 1.
DR MINT; Q12009; -.
DR STRING; 4932.YDL201W; -.
DR iPTMnet; Q12009; -.
DR MaxQB; Q12009; -.
DR PaxDb; Q12009; -.
DR PRIDE; Q12009; -.
DR EnsemblFungi; YDL201W_mRNA; YDL201W; YDL201W.
DR GeneID; 851326; -.
DR KEGG; sce:YDL201W; -.
DR SGD; S000002360; TRM8.
DR VEuPathDB; FungiDB:YDL201W; -.
DR eggNOG; KOG3115; Eukaryota.
DR GeneTree; ENSGT00390000017840; -.
DR HOGENOM; CLU_050910_3_1_1; -.
DR InParanoid; Q12009; -.
DR OMA; DLHNWMV; -.
DR BioCyc; YEAST:YDL201W-MON; -.
DR BRENDA; 2.1.1.33; 984.
DR UniPathway; UPA00989; -.
DR EvolutionaryTrace; Q12009; -.
DR PRO; PR:Q12009; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12009; protein.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0106143; C:tRNA (m7G46) methyltransferase complex; IDA:SGD.
DR GO; GO:0043527; C:tRNA methyltransferase complex; IPI:ComplexPortal.
DR GO; GO:0008176; F:tRNA (guanine-N7-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0036265; P:RNA (guanine-N7)-methylation; IBA:GO_Central.
DR GO; GO:0106004; P:tRNA (guanine-N7)-methylation; IDA:SGD.
DR GO; GO:0030488; P:tRNA methylation; IDA:ComplexPortal.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_03055; tRNA_methyltr_TrmB_euk; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR025763; Trm8_euk.
DR InterPro; IPR003358; tRNA_(Gua-N-7)_MeTrfase_Trmb.
DR PANTHER; PTHR23417; PTHR23417; 1.
DR PANTHER; PTHR23417:SF16; PTHR23417:SF16; 1.
DR Pfam; PF02390; Methyltransf_4; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00091; TIGR00091; 1.
DR PROSITE; PS51625; SAM_MT_TRMB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; S-adenosyl-L-methionine; Transferase;
KW tRNA processing; tRNA-binding.
FT CHAIN 1..286
FT /note="tRNA (guanine-N(7)-)-methyltransferase"
FT /id="PRO_0000171437"
FT ACT_SITE 184
FT /evidence="ECO:0000305"
FT BINDING 103
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03055,
FT ECO:0000269|PubMed:18184583"
FT BINDING 126..127
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 161..162
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 181
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03055,
FT ECO:0000269|PubMed:18184583"
FT BINDING 259..261
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MOD_RES 7
FT /note="Phosphoserine; by ATM or ATR"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 59
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:2VDU"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:2VDV"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:2VDU"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:2VDU"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 108..116
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 129..144
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:2VDU"
FT TURN 151..154
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 166..168
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 175..182
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 199..208
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 209..220
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 222..234
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 243..247
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 250..257
FT /evidence="ECO:0007829|PDB:2VDV"
FT HELIX 260..267
FT /evidence="ECO:0007829|PDB:2VDV"
FT STRAND 273..279
FT /evidence="ECO:0007829|PDB:2VDV"
SQ SEQUENCE 286 AA; 33391 MW; 0280B9A7B02C85B7 CRC64;
MKAKPLSQDP GSKRYAYRIN KEENRKELKH VKINESSLVQ EGQKIDLPKK RYYRQRAHSN
PFSDHQLEYP VSPQDMDWSK LYPYYKNAEN GQMTKKVTIA DIGCGFGGLM IDLSPAFPED
LILGMEIRVQ VTNYVEDRII ALRNNTASKH GFQNINVLRG NAMKFLPNFF EKGQLSKMFF
CFPDPHFKQR KHKARIITNT LLSEYAYVLK EGGVVYTITD VKDLHEWMVK HLEEHPLFER
LSKEWEENDE CVKIMRNATE EGKKVERKKG DKFVACFTRL PTPAIL
