TRM10_YEAST
ID TRM10_YEAST Reviewed; 293 AA.
AC Q12400; D6W1X5;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=tRNA (guanine(9)-N1)-methyltransferase {ECO:0000305|PubMed:12702816};
DE EC=2.1.1.221 {ECO:0000269|PubMed:12702816, ECO:0000269|PubMed:23793893};
DE AltName: Full=tRNA methyltransferase 10 {ECO:0000303|PubMed:12702816};
DE AltName: Full=tRNA(m1G9)-methyltransferase {ECO:0000303|PubMed:12702816};
DE Short=tRNA(m1G9)MTase {ECO:0000303|PubMed:12702816};
GN Name=TRM10 {ECO:0000303|PubMed:12702816};
GN OrderedLocusNames=YOL093W {ECO:0000312|SGD:S000005453}; ORFNames=O0926;
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 96604 / S288c / FY1679;
RX PubMed=8533473; DOI=10.1002/yea.320111009;
RA Zumstein E., Pearson B.M., Kalogeropoulos A., Schweizer M.;
RT "A 29.425 kb segment on the left arm of yeast chromosome XV contains more
RT than twice as many unknown as known open reading frames.";
RL Yeast 11:975-986(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
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 [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 FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12702816; DOI=10.1261/rna.5070303;
RA Jackman J.E., Montange R.K., Malik H.S., Phizicky E.M.;
RT "Identification of the yeast gene encoding the tRNA m1G methyltransferase
RT responsible for modification at position 9.";
RL RNA 9:574-585(2003).
RN [7]
RP FUNCTION.
RX PubMed=15640439; DOI=10.1093/nar/gni002;
RA Hiley S.L., Jackman J.E., Babak T., Trochesset M., Morris Q.D.,
RA Phizicky E.M., Hughes T.R.;
RT "Detection and discovery of RNA modifications using microarrays.";
RL Nucleic Acids Res. 33:E2-E2(2005).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16, AND IDENTIFICATION BY
RP 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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-283, 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 [10]
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 [11]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23793893; DOI=10.1261/rna.039651.113;
RA Swinehart W.E., Henderson J.C., Jackman J.E.;
RT "Unexpected expansion of tRNA substrate recognition by the yeast m1G9
RT methyltransferase Trm10.";
RL RNA 19:1137-1146(2013).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF 84-276 IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, AND
RP MUTAGENESIS OF GLN-118; VAL-209; ASP-210; LYS-211; ASN-212 AND THR-247.
RX PubMed=24081582; DOI=10.1093/nar/gkt869;
RA Shao Z., Yan W., Peng J., Zuo X., Zou Y., Li F., Gong D., Ma R., Wu J.,
RA Shi Y., Zhang Z., Teng M., Li X., Gong Q.;
RT "Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the
RT catalytic mechanism and recognition of tRNA substrate.";
RL Nucleic Acids Res. 42:509-525(2014).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent guanine N(1)-
CC methyltransferase that catalyzes the formation of N(1)-methylguanine at
CC position 9 (m1G9) in cytoplasmic tRNAs. {ECO:0000269|PubMed:12702816,
CC ECO:0000269|PubMed:15640439, ECO:0000269|PubMed:23793893}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(9) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-
CC methylguanosine(9) in tRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43156, Rhea:RHEA-COMP:10367, Rhea:RHEA-COMP:10368,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:73542, ChEBI:CHEBI:74269; EC=2.1.1.221;
CC Evidence={ECO:0000269|PubMed:12702816, ECO:0000269|PubMed:23793893};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2400 nM for tRNA(Gly GCC) {ECO:0000269|PubMed:23793893};
CC KM=1860 nM for tRNA(Val UAC) {ECO:0000269|PubMed:23793893};
CC Note=kcat is 0.54 min(-1) for tRNA(Gly GCC) and 0.31 min(-1) for
CC tRNA(Val UAC) (m1G9)-methylation, respectively.
CC {ECO:0000269|PubMed:23793893};
CC -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:O14214}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 4090 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class IV-like SAM-binding methyltransferase
CC superfamily. TRM10 family. {ECO:0000255|PROSITE-ProRule:PRU01012}.
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DR EMBL; X83121; CAA58186.1; -; Genomic_DNA.
DR EMBL; Z74835; CAA99105.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10691.1; -; Genomic_DNA.
DR PIR; S57376; S57376.
DR RefSeq; NP_014548.1; NM_001183347.1.
DR PDB; 4JWJ; X-ray; 1.76 A; A/B=84-276.
DR PDBsum; 4JWJ; -.
DR AlphaFoldDB; Q12400; -.
DR SMR; Q12400; -.
DR BioGRID; 34309; 93.
DR DIP; DIP-4737N; -.
DR IntAct; Q12400; 1.
DR MINT; Q12400; -.
DR STRING; 4932.YOL093W; -.
DR iPTMnet; Q12400; -.
DR MaxQB; Q12400; -.
DR PaxDb; Q12400; -.
DR PRIDE; Q12400; -.
DR EnsemblFungi; YOL093W_mRNA; YOL093W; YOL093W.
DR GeneID; 854060; -.
DR KEGG; sce:YOL093W; -.
DR SGD; S000005453; TRM10.
DR VEuPathDB; FungiDB:YOL093W; -.
DR eggNOG; KOG2967; Eukaryota.
DR GeneTree; ENSGT00530000063169; -.
DR HOGENOM; CLU_034384_1_0_1; -.
DR InParanoid; Q12400; -.
DR OMA; FKKNDGW; -.
DR BioCyc; MetaCyc:G3O-33493-MON; -.
DR BioCyc; YEAST:G3O-33493-MON; -.
DR BRENDA; 2.1.1.221; 984.
DR PRO; PR:Q12400; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q12400; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0052905; F:tRNA (guanine(9)-N(1))-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0016423; F:tRNA (guanine) methyltransferase activity; IDA:SGD.
DR GO; GO:0009019; F:tRNA (guanine-N1-)-methyltransferase activity; EXP:Reactome.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IDA:SGD.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0002939; P:tRNA N1-guanine methylation; IBA:GO_Central.
DR Gene3D; 3.40.1280.30; -; 1.
DR InterPro; IPR028564; MT_TRM10-typ.
DR InterPro; IPR038459; MT_TRM10-typ_sf.
DR InterPro; IPR016653; TRM10/TRM10A.
DR InterPro; IPR007356; tRNA_m1G_MeTrfase_euk.
DR InterPro; IPR016009; tRNA_MeTrfase_TRMD/TRM10.
DR PANTHER; PTHR13563; PTHR13563; 1.
DR PANTHER; PTHR13563:SF13; PTHR13563:SF13; 1.
DR Pfam; PF01746; tRNA_m1G_MT; 1.
DR PIRSF; PIRSF016323; tRNA_m1G_mtfrase_met; 1.
DR PROSITE; PS51675; SAM_MT_TRM10; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Cytoplasm; Methyltransferase; Nucleus;
KW Phosphoprotein; Reference proteome; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..293
FT /note="tRNA (guanine(9)-N1)-methyltransferase"
FT /id="PRO_0000060520"
FT DOMAIN 83..279
FT /note="SAM-dependent MTase TRM10-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01012"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 32..61
FT /evidence="ECO:0000255"
FT ACT_SITE 210
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:24081582"
FT BINDING 186..187
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 206
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 210..214
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 218
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 232
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 244..246
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MOD_RES 16
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 283
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MUTAGEN 118
FT /note="Q->A: Completely abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:24081582"
FT MUTAGEN 209
FT /note="V->A: Reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:24081582"
FT MUTAGEN 210
FT /note="D->N: Completely abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:24081582"
FT MUTAGEN 211
FT /note="K->A: Reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:24081582"
FT MUTAGEN 212
FT /note="N->A: Has weaker affinity for S-adenosyl-L-
FT methionine and reduces catalytic activity by 90%."
FT /evidence="ECO:0000269|PubMed:24081582"
FT MUTAGEN 247
FT /note="T->A: Reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:24081582"
FT STRAND 91..100
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 109..128
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 129..139
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 142..150
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 170..173
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 217..225
FT /evidence="ECO:0007829|PDB:4JWJ"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 248..258
FT /evidence="ECO:0007829|PDB:4JWJ"
FT TURN 259..262
FT /evidence="ECO:0007829|PDB:4JWJ"
FT HELIX 264..271
FT /evidence="ECO:0007829|PDB:4JWJ"
SQ SEQUENCE 293 AA; 34520 MW; C3DC7C4BB2FFBE63 CRC64;
MSNDEINQNE EKVKRTPPLP PVPEGMSKKQ WKKMCKRQRW EENKAKYNAE RRVKKKRLRH
ERSAKIQEYI DRGEEVPQEL IREPRINVNQ TDSGIEIILD CSFDELMNDK EIVSLSNQVT
RAYSANRRAN HFAEIKVAPF DKRLKQRFET TLKNTNYENW NHFKFLPDDK IMFGDEHISK
DKIVYLTADT EEKLEKLEPG MRYIVGGIVD KNRYKELCLK KAQKMGIPTR RLPIDEYINL
EGRRVLTTTH VVQLMLKYFD DHNWKNAFES VLPPRKLDAE AKSASSSPAP KDT
