BN3D2_RAT
ID BN3D2_RAT Reviewed; 285 AA.
AC D4ABH7;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 20-APR-2010, sequence version 1.
DT 03-AUG-2022, entry version 66.
DE RecName: Full=RNA 5'-monophosphate methyltransferase {ECO:0000305};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q7Z5W3};
DE AltName: Full=BCDIN3 domain-containing protein;
GN Name=Bcdin3d {ECO:0000312|RGD:1306433};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
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 -!- SUBUNIT: Interacts with DICER1; the interaction may be mediated by RNA.
CC {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; CH474035; EDL86984.1; -; Genomic_DNA.
DR RefSeq; NP_001102221.1; NM_001108751.1.
DR AlphaFoldDB; D4ABH7; -.
DR SMR; D4ABH7; -.
DR STRING; 10116.ENSRNOP00000040497; -.
DR PaxDb; D4ABH7; -.
DR Ensembl; ENSRNOT00000091538; ENSRNOP00000070196; ENSRNOG00000058430.
DR GeneID; 363001; -.
DR KEGG; rno:363001; -.
DR CTD; 144233; -.
DR RGD; 1306433; Bcdin3d.
DR eggNOG; KOG2899; Eukaryota.
DR GeneTree; ENSGT00940000153993; -.
DR HOGENOM; CLU_082749_0_0_1; -.
DR InParanoid; D4ABH7; -.
DR OMA; GNFMNYY; -.
DR OrthoDB; 1185441at2759; -.
DR PhylomeDB; D4ABH7; -.
DR TreeFam; TF324061; -.
DR PRO; PR:D4ABH7; -.
DR Proteomes; UP000002494; Chromosome 7.
DR Proteomes; UP000234681; Chromosome 7.
DR Bgee; ENSRNOG00000058430; Expressed in thymus and 20 other tissues.
DR Genevisible; D4ABH7; RN.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0008171; F:O-methyltransferase activity; ISO:RGD.
DR GO; GO:0070883; F:pre-miRNA binding; IEA:Ensembl.
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:0008175; F:tRNA methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0010586; P:miRNA metabolic process; ISO:RGD.
DR GO; GO:2000632; P:negative regulation of pre-miRNA processing; ISS:UniProtKB.
DR GO; GO:0031054; P:pre-miRNA processing; IEA:Ensembl.
DR GO; GO:0001510; P:RNA methylation; ISO:RGD.
DR GO; GO:0030488; P:tRNA methylation; 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..285
FT /note="RNA 5'-monophosphate methyltransferase"
FT /id="PRO_0000420469"
FT DOMAIN 53..275
FT /note="Bin3-type SAM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00848"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 46
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 77
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 111
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 136..137
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
FT BINDING 165
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q7Z5W3"
SQ SEQUENCE 285 AA; 32002 MW; 283E1621BD2CEF73 CRC64;
MAATQELSKG GVEEAVEEDD PAALKPGAAP FGNFPHYSRF HPPEQRLRLL PPELLRQLFP
PEGPERRPIL GLDVGCNSGD LSMALYKHFL SPHDGETSSG TSRELRLLCC DIDPVLVERA
ENGCRFPDAL TFITLDIMDQ ESRKVPLSSF LSQFGRSVFD IVFCMSVTMW IHLNHGDRGL
CEFLAHVSSL CSYLLVEPQP WKCYRAAARR LRKLGLHNFD HFRSLAIRGD MASQIVRILT
QDHGMELACC FGNTSWDRSL LLFRAKHTEE TQAIPESSTK ETGTD
