NSUN3_DANRE
ID NSUN3_DANRE Reviewed; 367 AA.
AC Q4KMK0; F6NJM6; Q6DG64;
DT 29-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 18-JAN-2017, sequence version 2.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial {ECO:0000250|UniProtKB:Q9H649};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q9H649};
DE AltName: Full=NOL1/NOP2/Sun domain family member 3 {ECO:0000250|UniProtKB:Q9H649};
GN Name=nsun3 {ECO:0000250|UniProtKB:Q9H649};
GN ORFNames=zgc:109983 {ECO:0000303|Ref.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).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Eye;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Mitochondrial tRNA methyltransferase that mediates
CC methylation of cytosine to 5-methylcytosine (m5C) at position 34 of mt-
CC tRNA(Met). mt-tRNA(Met) methylation at cytosine(34) takes place at the
CC wobble position of the anticodon and initiates the formation of 5-
CC formylcytosine (f(5)c) at this position. mt-tRNA(Met) containing the
CC f(5)c modification at the wobble position enables recognition of the
CC AUA codon in addition to the AUG codon, expanding codon recognition in
CC mitochondrial translation. {ECO:0000250|UniProtKB:Q9H649}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(34) in mitochondrial tRNA + S-adenosyl-L-methionine =
CC 5-methylcytidine(34) in mitochondrial tRNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:53076, Rhea:RHEA-COMP:13451, Rhea:RHEA-
CC COMP:13453, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000250|UniProtKB:Q9H649};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53077;
CC Evidence={ECO:0000250|UniProtKB:Q9H649};
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000250|UniProtKB:Q9H649}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|PROSITE-ProRule:PRU01023}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH76487.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CR762462; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CU915566; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; CR762462; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CU915566; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC076487; AAH76487.1; ALT_INIT; mRNA.
DR EMBL; BC098531; AAH98531.1; -; mRNA.
DR RefSeq; NP_001020473.1; NM_001025302.1.
DR AlphaFoldDB; Q4KMK0; -.
DR SMR; Q4KMK0; -.
DR STRING; 7955.ENSDARP00000118143; -.
DR PaxDb; Q4KMK0; -.
DR GeneID; 553534; -.
DR KEGG; dre:553534; -.
DR CTD; 63899; -.
DR ZFIN; ZDB-GENE-050706-95; nsun3.
DR eggNOG; KOG2198; Eukaryota.
DR InParanoid; Q4KMK0; -.
DR OrthoDB; 1239772at2759; -.
DR PhylomeDB; Q4KMK0; -.
DR TreeFam; TF321304; -.
DR PRO; PR:Q4KMK0; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005762; C:mitochondrial large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0005759; C:mitochondrial matrix; ISS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR GO; GO:0008168; F:methyltransferase activity; IBA:GO_Central.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0070129; P:regulation of mitochondrial translation; ISS:UniProtKB.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0031167; P:rRNA methylation; IBA:GO_Central.
DR GO; GO:0002127; P:tRNA wobble base cytosine methylation; ISS:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22808; PTHR22808; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 2: Evidence at transcript level;
KW Methyltransferase; Mitochondrion; Reference proteome; RNA-binding;
KW S-adenosyl-L-methionine; Transferase; tRNA-binding.
FT CHAIN 1..367
FT /note="tRNA (cytosine(34)-C(5))-methyltransferase,
FT mitochondrial"
FT /id="PRO_0000289232"
FT ACT_SITE 296
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 170..176
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 193
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 224
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 242
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT CONFLICT 30
FT /note="Missing (in Ref. 2; AAH76487)"
FT /evidence="ECO:0000305"
FT CONFLICT 50
FT /note="Y -> H (in Ref. 2; AAH98531)"
FT /evidence="ECO:0000305"
FT CONFLICT 322
FT /note="L -> M (in Ref. 2; AAH98531)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 367 AA; 41270 MW; CDD55B2BD98299D1 CRC64;
MSGSSFLFLK SIKCILSSSC HGQNTISNTQ LAAQYISKPQ KQLCETVLKY FDRQYSEELG
EQWWNARDVL LNPLSWQYGV LLNRFSDLTN LKQCLAELGY TNLLQQTHPE SHSQTADIPL
QCFIHPDPVR IPTQSHHTGW LKQYYLLNAA SLLPVLALNV QEGENVLDLC AAPGGKSLAI
LQTATPGLLH CNEVDQHRHD WLLKTLESYV PPSLRHLLSV TLQDGRSIGT MQPGAYDKVL
VDAPCSNDRS WLYTPDTHRG EMWLKERTQL PLLQKELLCS ALAAVRPGGI VVYSTCTMSR
AENQSVVEEV LASYPGVELQ ELEQQFIDSL SDHFCFAHLH PSVGQLVIPQ KGKTWGPMYV
SQLKKIY
