TRM2A_MOUSE
ID TRM2A_MOUSE Reviewed; 613 AA.
AC Q8BNV1; P70221; P70222; Q3UYU2; Q78E15; Q80VN8;
DT 16-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 25-MAY-2022, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=tRNA (uracil-5-)-methyltransferase homolog A {ECO:0000305};
DE EC=2.1.1.35 {ECO:0000250|UniProtKB:Q8IZ69};
DE AltName: Full=HpaII tiny fragments locus 9c protein {ECO:0000303|PubMed:1889746};
DE AltName: Full=mRNA (uracil-5-)-methyltransferase TRMT2A {ECO:0000305};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q8IZ69};
GN Name=Trmt2a {ECO:0000312|MGI:MGI:96270};
GN Synonyms=Htf9-c {ECO:0000303|PubMed:1889746},
GN Htf9c {ECO:0000303|PubMed:1889746};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=1889746; DOI=10.1016/0378-1119(91)90274-f;
RA Bressan A., Somma M.P., Lewis J., Santolamazza C., Copeland N.G.,
RA Gilbert D.J., Jenkins N.A., Lavia P.;
RT "Characterization of the opposite-strand genes from the mouse
RT bidirectionally transcribed HTF9 locus.";
RL Gene 103:201-209(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROMOTER ORGANIZATION, AND
RP INDUCTION.
RC STRAIN=C57BL/6J;
RX PubMed=9224656; DOI=10.1042/bj3250277;
RA Guarguaglini G., Battistoni A., Pittoggi C., Di Matteo G., Di Fiore B.,
RA Lavia P.;
RT "Expression of the murine RanBP1 and Htf9-c genes is regulated from a
RT shared bidirectional promoter during cell cycle progression.";
RL Biochem. J. 325:277-286(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=C57BL/6J; TISSUE=Aorta, Bone marrow, Testis, and Vein;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Olfactory epithelium;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP PROMOTER ORGANIZATION, TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=9417108; DOI=10.1074/jbc.273.1.495;
RA Di Matteo G., Salerno M., Guarguaglini G., Di Fiore B., Palitti F.,
RA Lavia P.;
RT "Interactions with single-stranded and double-stranded DNA-binding factors
RT and alternative promoter conformation upon transcriptional activation of
RT the Htf9-a/RanBP1 and Htf9-c genes.";
RL J. Biol. Chem. 273:495-505(1998).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Lung, Pancreas, Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
CC catalyzes the formation of 5-methyl-uridine in tRNAs and some mRNAs.
CC Mainly catalyzes the methylation of uridine at position 54 (m5U54) in
CC cytosolic tRNAs. Also able to mediate the formation of 5-methyl-uridine
CC in some mRNAs. {ECO:0000250|UniProtKB:Q8IZ69}.
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:0000250|UniProtKB:Q8IZ69};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42713;
CC Evidence={ECO:0000250|UniProtKB:Q8IZ69};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a uridine in mRNA + S-adenosyl-L-methionine = a 5-
CC methyluridine in mRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:69863, Rhea:RHEA-COMP:14658, Rhea:RHEA-COMP:17793,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447;
CC Evidence={ECO:0000250|UniProtKB:Q8IZ69};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:69864;
CC Evidence={ECO:0000250|UniProtKB:Q8IZ69};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:Q8IZ69}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8BNV1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BNV1-2; Sequence=VSP_061469;
CC -!- TISSUE SPECIFICITY: Widely expressed at low level. Expressed at higher
CC level in proliferating cells. {ECO:0000269|PubMed:9417108}.
CC -!- INDUCTION: In a cell-cycle manner (PubMed:9224656, PubMed:9417108).
CC Transcription is activated at the G1/S transition of the cell cycle and
CC peaks in S phase, while being repressed in quiescent tissues and
CC growth-arrested cells (PubMed:9417108). {ECO:0000269|PubMed:9224656,
CC ECO:0000269|PubMed:9417108}.
CC -!- MISCELLANEOUS: Htf9a (RanBP1) and Trmt2a are transcribed with opposite
CC polarity from complementary DNA strands from a shared bidirectional
CC TATA-less promoter. {ECO:0000269|PubMed:1889746,
CC ECO:0000269|PubMed:9417108}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01024}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH46976.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X05830; CAA29277.1; -; Genomic_DNA.
DR EMBL; X56044; CAA39515.1; -; mRNA.
DR EMBL; AK080170; BAC37838.1; -; mRNA.
DR EMBL; AK153190; BAE31790.1; -; mRNA.
DR EMBL; AK133844; BAE21880.1; -; mRNA.
DR EMBL; AK134368; BAE22119.1; -; mRNA.
DR EMBL; AK150482; BAE29598.1; -; mRNA.
DR EMBL; AK151311; BAE30293.1; -; mRNA.
DR EMBL; AK151422; BAE30387.1; -; mRNA.
DR EMBL; AK151725; BAE30643.1; -; mRNA.
DR EMBL; AK151778; BAE30683.1; -; mRNA.
DR EMBL; AK152055; BAE30911.1; -; mRNA.
DR EMBL; AK152201; BAE31030.1; -; mRNA.
DR EMBL; AK152363; BAE31153.1; -; mRNA.
DR EMBL; AK152548; BAE31303.1; -; mRNA.
DR EMBL; AK152903; BAE31584.1; -; mRNA.
DR EMBL; AK153043; BAE31672.1; -; mRNA.
DR EMBL; BC046976; AAH46976.1; ALT_INIT; mRNA.
DR CCDS; CCDS57020.1; -. [Q8BNV1-1]
DR PIR; S01176; S01176.
DR RefSeq; NP_001074468.1; NM_001080999.2.
DR RefSeq; NP_001074469.1; NM_001081000.2.
DR RefSeq; NP_001182134.1; NM_001195205.1.
DR AlphaFoldDB; Q8BNV1; -.
DR SMR; Q8BNV1; -.
DR BioGRID; 200464; 1.
DR IntAct; Q8BNV1; 1.
DR MINT; Q8BNV1; -.
DR STRING; 10090.ENSMUSP00000111304; -.
DR PhosphoSitePlus; Q8BNV1; -.
DR EPD; Q8BNV1; -.
DR MaxQB; Q8BNV1; -.
DR PeptideAtlas; Q8BNV1; -.
DR PRIDE; Q8BNV1; -.
DR ProteomicsDB; 298315; -.
DR ProteomicsDB; 336881; -.
DR Antibodypedia; 250; 340 antibodies from 26 providers.
DR DNASU; 15547; -.
DR Ensembl; ENSMUST00000115640; ENSMUSP00000111304; ENSMUSG00000022721. [Q8BNV1-1]
DR Ensembl; ENSMUST00000140206; ENSMUSP00000121216; ENSMUSG00000022721. [Q8BNV1-2]
DR GeneID; 15547; -.
DR KEGG; mmu:15547; -.
DR UCSC; uc007ync.2; mouse. [Q8BNV1-1]
DR CTD; 27037; -.
DR MGI; MGI:96270; Trmt2a.
DR VEuPathDB; HostDB:ENSMUSG00000022721; -.
DR eggNOG; KOG2187; Eukaryota.
DR GeneTree; ENSGT00530000063723; -.
DR HOGENOM; CLU_014689_4_2_1; -.
DR InParanoid; Q8BNV1; -.
DR OrthoDB; 248059at2759; -.
DR PhylomeDB; Q8BNV1; -.
DR TreeFam; TF314569; -.
DR BioGRID-ORCS; 15547; 1 hit in 70 CRISPR screens.
DR ChiTaRS; Trmt2a; mouse.
DR PRO; PR:Q8BNV1; -.
DR Proteomes; UP000000589; Chromosome 16.
DR RNAct; Q8BNV1; protein.
DR Bgee; ENSMUSG00000022721; Expressed in ventricular zone and 108 other tissues.
DR ExpressionAtlas; Q8BNV1; baseline and differential.
DR Genevisible; Q8BNV1; MM.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0008169; F:C-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:1901564; P:organonitrogen compound metabolic process; IEA:UniProt.
DR CDD; cd12439; RRM_TRMT2A; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR045850; TRM2_euk.
DR InterPro; IPR034262; TRMT2A_RRM.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR45904; PTHR45904; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Coiled coil; Cytoplasm; Methyltransferase;
KW mRNA processing; Phosphoprotein; Reference proteome; RNA-binding;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..613
FT /note="tRNA (uracil-5-)-methyltransferase homolog A"
FT /id="PRO_0000081615"
FT DOMAIN 63..136
FT /note="RRM"
FT REGION 1..46
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 170..200
FT /evidence="ECO:0000255"
FT ACT_SITE 528
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT ACT_SITE 571
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P23003"
FT BINDING 401
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 451
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 500
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT MOD_RES 368
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8IZ69"
FT VAR_SEQ 468..507
FT /note="ELSNVEFHCGRAEDLVPGLVSRLSSHQLVAVLDPPRAGLH -> D (in
FT isoform 2)"
FT /id="VSP_061469"
FT CONFLICT 1..46
FT /note="MSEPAAEVPEPMEDCGQDASAVPSSAAPLCQKEEAGPGPAAGPGTQ -> MW
FT TGWAEVGWGSSHYCRIKDRMGENWVSRVKERVSPGLRGVCTNGDLSAVWGSESYQLEPS
FT ARPVCSHVGSGAHGGLRPGLPSCTPALRPHYVKKRKQGLGQLQGLERK (in Ref.
FT 1; CAA29277 and 2; CAA39515)"
FT /evidence="ECO:0000305"
FT CONFLICT 115
FT /note="A -> G (in Ref. 1; CAA29277 and 2; CAA39515)"
FT /evidence="ECO:0000305"
FT CONFLICT 130..145
FT /note="SVRLARPKADPMARKR -> AYAWPDPRLTPWLGRG (in Ref. 1;
FT CAA29277 and 2; CAA39515)"
FT /evidence="ECO:0000305"
FT CONFLICT 158..190
FT /note="IADVVTPLWTVPYTEQLEQKRLECERVLQKLAK -> SCRCGDPSVDTALHV
FT SSWSRSDWNVSGCYRNLAR (in Ref. 1; CAA29277 and 2; CAA39515)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 613 AA; 67488 MW; 6A677FE70848A809 CRC64;
MSEPAAEVPE PMEDCGQDAS AVPSSAAPLC QKEEAGPGPA AGPGTQPGLY SYIRDDLFTS
EIFKLELQNV PRHASFSDVR RFLGRFGLQS HKIKLFGQPP CAFVTFRSAA ERDKALRVLH
GALWKGCPLS VRLARPKADP MARKRRQEGD SEPSVTQIAD VVTPLWTVPY TEQLEQKRLE
CERVLQKLAK EIGNTNRALL PWLLLQRQQH NKACCPLEGV KPSPQQTEYR NKCEFLVGVG
VDGKDNTVGC RLGKYKGGTC AVAAPFDTVH IPEATKQVVK AFQEFIRSTP YSAYDPETYT
GHWKQLTVRT SSRGQAMAIA YFHPQKLSSE EVAGLKASLV CHFMEGPGKA SGVTSLYFVE
EGQRKTPSQE GLPLEHMAGD QCIQEDLLGL TFRISPHAFF QVNTPAAEVL YTVIQEWAQL
DGGSTVLDVC CGTGTIGLAL APKVKRVVGI ELCQEAVEDA RMNALTNELS NVEFHCGRAE
DLVPGLVSRL SSHQLVAVLD PPRAGLHSKV ILAIRKAENI KRLLYVSCNP RAAMGNFVDL
CRAPSNRVKG TPFHPVKAVA VDLFPQTPHC EMLILFERMQ QHPNGIEALE HQEFQTPRNL
PDITPQETEI SLS
