TRM9_ARATH
ID TRM9_ARATH Reviewed; 404 AA.
AC Q94A09; Q8LB98; Q9C8X9;
DT 31-JAN-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=tRNA (carboxymethyluridine(34)-5-O)-methyltransferase {ECO:0000305};
DE EC=2.1.1.229 {ECO:0000305|PubMed:21653555};
DE AltName: Full=tRNA methyltransferase 9 homolog {ECO:0000305};
DE Short=AtTRM9 {ECO:0000303|PubMed:21653555};
GN Name=TRM9 {ECO:0000303|PubMed:21653555};
GN OrderedLocusNames=At1g36310 {ECO:0000312|Araport:AT1G36310};
GN ORFNames=F7F23.3 {ECO:0000312|EMBL:AAG52197.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-238, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-238, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND INTERACTION WITH TRM112A AND TRM112B.
RX PubMed=21653555; DOI=10.1093/nar/gkr406;
RA Leihne V., Kirpekar F., Vaagboe C.B., van den Born E., Krokan H.E.,
RA Grini P.E., Meza T.J., Falnes P.O.;
RT "Roles of Trm9- and ALKBH8-like proteins in the formation of modified
RT wobble uridines in Arabidopsis tRNA.";
RL Nucleic Acids Res. 39:7688-7701(2011).
CC -!- FUNCTION: Catalyzes the methylation of 5-carboxymethyl uridine to 5-
CC methylcarboxymethyl uridine at the wobble position of the anticodon
CC loop in tRNA via its methyltransferase domain. Catalyzes the last step
CC in the formation of 5-methylcarboxymethyl uridine at the wobble
CC position of the anticodon loop in target tRNA.
CC {ECO:0000269|PubMed:21653555}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=carboxymethyluridine(34) in tRNA + S-adenosyl-L-methionine =
CC 5-(2-methoxy-2-oxoethyl)uridine(34) in tRNA + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43208, Rhea:RHEA-COMP:10407, Rhea:RHEA-
CC COMP:10408, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74851,
CC ChEBI:CHEBI:74882; EC=2.1.1.229;
CC Evidence={ECO:0000305|PubMed:21653555};
CC -!- SUBUNIT: Interacts with TRM112A and TRM112B.
CC {ECO:0000269|PubMed:21653555}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG52197.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAM64893.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC021199; AAG52197.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE31858.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31859.1; -; Genomic_DNA.
DR EMBL; AY050771; AAK92706.1; -; mRNA.
DR EMBL; AY091371; AAM14310.1; -; mRNA.
DR EMBL; AK317228; BAH19909.1; -; mRNA.
DR EMBL; AY087343; AAM64893.1; ALT_INIT; mRNA.
DR PIR; C86484; C86484.
DR RefSeq; NP_001031144.1; NM_001036067.2.
DR RefSeq; NP_564470.1; NM_103320.3.
DR AlphaFoldDB; Q94A09; -.
DR SMR; Q94A09; -.
DR STRING; 3702.AT1G36310.1; -.
DR iPTMnet; Q94A09; -.
DR PaxDb; Q94A09; -.
DR PRIDE; Q94A09; -.
DR ProteomicsDB; 228720; -.
DR EnsemblPlants; AT1G36310.1; AT1G36310.1; AT1G36310.
DR EnsemblPlants; AT1G36310.2; AT1G36310.2; AT1G36310.
DR GeneID; 840538; -.
DR Gramene; AT1G36310.1; AT1G36310.1; AT1G36310.
DR Gramene; AT1G36310.2; AT1G36310.2; AT1G36310.
DR KEGG; ath:AT1G36310; -.
DR Araport; AT1G36310; -.
DR TAIR; locus:2035947; AT1G36310.
DR eggNOG; KOG1331; Eukaryota.
DR HOGENOM; CLU_029501_1_0_1; -.
DR InParanoid; Q94A09; -.
DR OMA; INICAER; -.
DR OrthoDB; 996085at2759; -.
DR PhylomeDB; Q94A09; -.
DR PRO; PR:Q94A09; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94A09; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
DR GO; GO:0106335; F:tRNA (carboxymethyluridine(34)-5-O)-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IDA:TAIR.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IMP:TAIR.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR013216; Methyltransf_11.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF08241; Methyltransf_11; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Phosphoprotein; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..404
FT /note="tRNA (carboxymethyluridine(34)-5-O)-
FT methyltransferase"
FT /id="PRO_0000443081"
FT MOD_RES 238
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
SQ SEQUENCE 404 AA; 44960 MW; 102AD115EA29881C CRC64;
MILDVLRTFS TRTRNLPSSG FYSISTSIMR DIKVKSDSKE FLTSSDEEEE SVSIRVSSSS
SLSSVKSTPE IEKKYVHRVY DAIAPHFSST RFAKWPKVAA FLESLPSGSV ILDAGCGNGK
YLGLNPSCFF IGCDISHPLI KICSDKGQEV LVADAVNLPY REEFGDAAIS IAVLHHLSTE
NRRKKAIEEL VRVVKPGGFV LITVWAAEQE DTSLLTKWTP LSAKYVEEWV GPGSPMNSPR
VRNNPFFSLE SIPETEVSTK EQKVENSQFI GLESIPESEE STREQKGESI IPETKASIVE
QKDEKSVEES LEALKKSQQE YFVPWHLPYH RAEVSGASAS ALASGLAKKD DRKGAVVYNR
YYHVFSEGEL ERLASGVGNA MIVDRFFDKS NWCIVLQKEA LNQD
