BN3D2_DANRE
ID BN3D2_DANRE Reviewed; 254 AA.
AC A8E7D2; F1QAZ2; F1QCI6;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 28-NOV-2012, sequence version 2.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Pre-miRNA 5'-monophosphate methyltransferase;
DE EC=2.1.1.-;
DE AltName: Full=BCDIN3 domain-containing protein;
GN Name=bcdin3d; ORFNames=si:dkey-222f2.2;
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).
CC -!- FUNCTION: O-methyltransferase that specifically monomethylates 5'-
CC monophosphate of cytoplasmic histidyl tRNA (tRNA(His)), acting as a
CC capping enzyme by protecting tRNA(His) from cleavage by DICER1. Also
CC able, with less efficiently, to methylate the 5' monophosphate of a
CC subset of pre-miRNAs, acting as a negative regulator of miRNA
CC processing. The 5' monophosphate of pre-miRNAs is recognized by DICER1
CC and is required for pre-miRNAs processing: methylation at this position
CC reduces the processing of pre-miRNAs by DICER1. Was also reported to
CC mediate dimethylation of pre-miR-145; however dimethylation cannot be
CC reproduced by another group which observes a monomethylation of pre-
CC miR-145. {ECO:0000250|UniProtKB:Q7Z5W3}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (5'-phospho)-ribonucleoside-RNA + S-adenosyl-L-
CC methionine = a 5'-end (5'-methylphospho)-ribonucleoside-RNA + S-
CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:58656, Rhea:RHEA-COMP:15179,
CC Rhea:RHEA-COMP:15181, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:142776;
CC Evidence={ECO:0000250|UniProtKB:Q7Z5W3};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (5'-phospho)-ribonucleoside-RNA + 2 S-adenosyl-L-
CC methionine = a 5'-end (5'-bismethylphospho)-ribonucleoside-RNA + 2 S-
CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:58640, Rhea:RHEA-COMP:15179,
CC Rhea:RHEA-COMP:15182, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:142777;
CC Evidence={ECO:0000250|UniProtKB:Q7Z5W3};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q7Z5W3}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily.
CC {ECO:0000305}.
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DR EMBL; BX005329; CAP09428.1; -; Genomic_DNA.
DR RefSeq; XP_017208938.1; XM_017353449.1.
DR AlphaFoldDB; A8E7D2; -.
DR SMR; A8E7D2; -.
DR STRING; 7955.ENSDARP00000098771; -.
DR PaxDb; A8E7D2; -.
DR GeneID; 568375; -.
DR KEGG; dre:568375; -.
DR ZFIN; ZDB-GENE-050208-327; bcdin3d.
DR eggNOG; KOG2899; Eukaryota.
DR InParanoid; A8E7D2; -.
DR OrthoDB; 1185441at2759; -.
DR PRO; PR:A8E7D2; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0008171; F:O-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0008173; F:RNA methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0090486; F:small RNA 2'-O-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0010586; P:miRNA metabolic process; IBA:GO_Central.
DR GO; GO:2000632; P:negative regulation of pre-miRNA processing; ISS:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR039772; Bin3-like.
DR InterPro; IPR010675; Bin3_C.
DR InterPro; IPR024160; BIN3_SAM-bd_dom.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR12315; PTHR12315; 1.
DR Pfam; PF06859; Bin3; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51515; BIN3_SAM; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..254
FT /note="Pre-miRNA 5'-monophosphate methyltransferase"
FT /id="PRO_0000420470"
FT DOMAIN 34..254
FT /note="Bin3-type SAM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00848"
FT BINDING 36
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 66
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 99
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 124..125
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
SQ SEQUENCE 254 AA; 28819 MW; D4ECFFCE950A467A CRC64;
MEAHDAHVNS EESENPGAAP YGNFINYYTF NPPENRLSLI PEALLQNIGF TSGDGERVLM
LDVGCNSGDL SVALYKHLLN KEACTSDSPR QELYMLGFDL DQDLILRAQT SNPFPQNIQF
IPLDITDDTE SRAVLQAFLG KFGCSRFHLS TCFAVTMWVH LNHGDAAFLS LLSRLASHSE
YLLLEAQPWK CYRSAARRLR KLGRSDFDHF KALKIRGDMA AHAREHLEKQ CSMELVQCFG
NTSWDRSLLL FRRQ
