TRM2B_DANRE
ID TRM2B_DANRE Reviewed; 480 AA.
AC A4QP75; B7ZD53;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2010, sequence version 2.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=tRNA (uracil-5-)-methyltransferase homolog B;
DE EC=2.1.1.35 {ECO:0000250|UniProtKB:Q96GJ1};
DE AltName: Full=TRM2 homolog B {ECO:0000305};
DE AltName: Full=rRNA (uracil-5-)-methyltransferase TRMT2B {ECO:0000305};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q96GJ1};
DE Flags: Precursor;
GN Name=trmt2b; ORFNames=si:dkeyp-115d2.4, zgc:162982;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Ovary;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Mitochondrial S-adenosyl-L-methionine-dependent
CC methyltransferase that catalyzes the formation of 5-methyl-uridine in
CC tRNAs and 12S rRNA. Catalyzes the methylation of uridine at position 54
CC (m5U54) in all tRNAs. Specifically methylates the uridine in position
CC 429 of 12S rRNA (m5U429). Does not affect RNA stability or
CC mitochondrial translation. {ECO:0000250|UniProtKB:Q96GJ1}.
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:Q96GJ1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42713;
CC Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a uridine in 12S rRNA + S-adenosyl-L-methionine = a 5-
CC methyluridine in 12S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:69859, Rhea:RHEA-COMP:17791, Rhea:RHEA-COMP:17792,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447;
CC Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:69860;
CC Evidence={ECO:0000250|UniProtKB:Q96GJ1};
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250|UniProtKB:Q96GJ1}.
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=AAI39683.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL929344; CAX12082.1; -; Genomic_DNA.
DR EMBL; BC139682; AAI39683.1; ALT_INIT; mRNA.
DR RefSeq; NP_001116415.1; NM_001122943.1.
DR AlphaFoldDB; A4QP75; -.
DR SMR; A4QP75; -.
DR STRING; 7955.ENSDARP00000112957; -.
DR PaxDb; A4QP75; -.
DR PeptideAtlas; A4QP75; -.
DR Ensembl; ENSDART00000143745; ENSDARP00000112957; ENSDARG00000033967.
DR GeneID; 606657; -.
DR KEGG; dre:606657; -.
DR CTD; 79979; -.
DR ZFIN; ZDB-GENE-050809-101; trmt2b.
DR eggNOG; KOG2187; Eukaryota.
DR GeneTree; ENSGT00530000063723; -.
DR InParanoid; A4QP75; -.
DR OrthoDB; 248059at2759; -.
DR PhylomeDB; A4QP75; -.
DR TreeFam; TF352239; -.
DR PRO; PR:A4QP75; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 13.
DR Bgee; ENSDARG00000033967; Expressed in presomitic mesoderm and 24 other tissues.
DR ExpressionAtlas; A4QP75; baseline.
DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; ISS:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR045850; TRM2_euk.
DR InterPro; IPR025823; tRNA_(uracil-5-)_MeTrfase_met.
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 PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
PE 2: Evidence at transcript level;
KW Methyltransferase; Mitochondrion; Reference proteome; rRNA processing;
KW S-adenosyl-L-methionine; Transferase; Transit peptide; tRNA processing.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN ?..480
FT /note="tRNA (uracil-5-)-methyltransferase homolog B"
FT /id="PRO_0000311935"
FT ACT_SITE 427
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT ACT_SITE 473
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P23003"
FT BINDING 299
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 349
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 399
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
SQ SEQUENCE 480 AA; 53895 MW; F8B46A9DCC7047F8 CRC64;
MSSAFKAMRL HLTCPLPKQV INIPQTLFSY LITNQRAINN SCKPVKTSNA KKPKLPTTKL
SWEERLSDTV TPLWRMTYED QLQWKYEHQK KILLKMMKEL SQDPTRAFSD HLNFPLLPIV
ASPVRDGYRN KSTFSVNKGI DGNPKTLGFY IGTGKAGNIV CVHADHLLSI PSKHKMVARC
YEDFIRLSPL RPCILFDDGG HWREITIRTN STGHTMAIVY FHPQSLTPEE TDIHKAALVE
YFTQGPGAIC QLDSLYFQET TMTRCSHEQS QYQLLYGQTH IYEEVLGFKF RISPDSFFQV
NREAAEALYK TVAELSQPCV GGTLLDVCCG TGAIGISLSP QMERVIGIEL IEQAVEDAKF
NAALNRVCNC EFLAGKAEVV LPDLMGSLSS DGGLTAVVNP SRAGLHYRVV RALRNHSAIR
RLVYISCKPD GEAMRNFREL CCSVGLVRRI TGEAFKPVVA VPVDLFPHTP HCELVLVFER
