MRM3_HUMAN
ID MRM3_HUMAN Reviewed; 420 AA.
AC Q9HC36; Q53GN1; Q86VC3; Q96F76; Q9NVQ5;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=rRNA methyltransferase 3, mitochondrial {ECO:0000303|PubMed:25009282};
DE EC=2.1.1.- {ECO:0000305|PubMed:24036117, ECO:0000305|PubMed:25074936};
DE AltName: Full=16S rRNA (guanosine(1370)-2'-O)-methyltransferase {ECO:0000303|PubMed:25074936};
DE AltName: Full=16S rRNA [Gm1370] 2'-O-methyltransferase {ECO:0000303|PubMed:25074936};
DE AltName: Full=RNA methyltransferase-like protein 1 {ECO:0000303|PubMed:12296377};
DE Flags: Precursor;
GN Name=MRM3 {ECO:0000303|PubMed:25009282, ECO:0000312|HGNC:HGNC:18485};
GN Synonyms=RNMTL1 {ECO:0000303|PubMed:12296377}; ORFNames=HC90;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Teratocarcinoma;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney;
RA Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y.,
RA Tanaka A., Yokoyama S.;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Gu J.R., Zhao X.T., Wan D.F., Jiang H.Q., Huang Y., He Y.H., Qin W.X.,
RA Han L.W., Zhang P.P., Qiu X.K., He L.P.;
RT "Homo sapiens P579 chromosome 17p DNA sequence fragment.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANTS SER-8 AND VAL-185.
RC TISSUE=Brain, and Skin;
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 TISSUE SPECIFICITY.
RX PubMed=12296377; DOI=10.1038/sj.cr.7290124;
RA Xu J., De Zhu J., Ni M., Wan F., Gu J.R.;
RT "The ATF/CREB site is the key element for transcription of the human RNA
RT methyltransferase like 1(RNMTL1) gene, a newly discovered 17p13.3 gene.";
RL Cell Res. 12:177-197(2002).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [8]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=24036117; DOI=10.1074/jbc.m113.515692;
RA Lee K.W., Okot-Kotber C., LaComb J.F., Bogenhagen D.F.;
RT "Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are
RT positioned to modify nascent rRNA in foci near the mitochondrial DNA
RT nucleoid.";
RL J. Biol. Chem. 288:31386-31399(2013).
RN [9]
RP FUNCTION.
RX PubMed=25074936; DOI=10.1074/jbc.c114.581868;
RA Lee K.W., Bogenhagen D.F.;
RT "Assignment of 2'-O-methyltransferases to modification sites on the
RT mammalian mitochondrial large subunit 16S rRNA.";
RL J. Biol. Chem. 289:24936-24942(2014).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [11]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=25009282; DOI=10.1091/mbc.e14-01-0014;
RA Rorbach J., Boesch P., Gammage P.A., Nicholls T.J., Pearce S.F., Patel D.,
RA Hauser A., Perocchi F., Minczuk M.;
RT "MRM2 and MRM3 are involved in biogenesis of the large subunit of the
RT mitochondrial ribosome.";
RL Mol. Biol. Cell 25:2542-2555(2014).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose
CC methyltransferase that catalyzes the formation of 2'-O-methylguanosine
CC at position 1370 (Gm1370) in the 16S mitochondrial large subunit
CC ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl
CC transferase domain of the mtLSU rRNA. {ECO:0000269|PubMed:24036117,
CC ECO:0000269|PubMed:25009282, ECO:0000269|PubMed:25074936}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(1370) in 16S rRNA + S-adenosyl-L-methionine = 2'-O-
CC methylguanosine(1370) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:47756, Rhea:RHEA-COMP:11899, Rhea:RHEA-COMP:11900,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74269, ChEBI:CHEBI:74445;
CC Evidence={ECO:0000305|PubMed:24036117, ECO:0000305|PubMed:25074936};
CC -!- INTERACTION:
CC Q9HC36; Q9NVV5-2: AIG1; NbExp=3; IntAct=EBI-1045440, EBI-11957045;
CC Q9HC36; Q8WVV5: BTN2A2; NbExp=3; IntAct=EBI-1045440, EBI-8648738;
CC Q9HC36; Q8WVX3-2: C4orf3; NbExp=3; IntAct=EBI-1045440, EBI-12003442;
CC Q9HC36; Q13643: FHL3; NbExp=8; IntAct=EBI-1045440, EBI-741101;
CC Q9HC36; Q05329: GAD2; NbExp=3; IntAct=EBI-1045440, EBI-9304251;
CC Q9HC36; Q10471: GALNT2; NbExp=3; IntAct=EBI-1045440, EBI-10226985;
CC Q9HC36; Q8N5M9: JAGN1; NbExp=3; IntAct=EBI-1045440, EBI-10266796;
CC Q9HC36; P30301: MIP; NbExp=3; IntAct=EBI-1045440, EBI-8449636;
CC Q9HC36; Q9HC36: MRM3; NbExp=3; IntAct=EBI-1045440, EBI-1045440;
CC Q9HC36; Q14162: SCARF1; NbExp=3; IntAct=EBI-1045440, EBI-12056025;
CC Q9HC36; P01375: TNF; NbExp=3; IntAct=EBI-1045440, EBI-359977;
CC Q9HC36; Q9Y5Z9: UBIAD1; NbExp=3; IntAct=EBI-1045440, EBI-2819725;
CC Q9HC36; O95159: ZFPL1; NbExp=3; IntAct=EBI-1045440, EBI-718439;
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:24036117,
CC ECO:0000269|PubMed:25009282}.
CC -!- TISSUE SPECIFICITY: Expressed at same level in normal liver and
CC hepatocarcinoma. {ECO:0000269|PubMed:12296377}.
CC -!- SIMILARITY: Belongs to the class IV-like SAM-binding methyltransferase
CC superfamily. RNA methyltransferase TrmH family. {ECO:0000305}.
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DR EMBL; AK001443; BAA91694.1; -; mRNA.
DR EMBL; AK222900; BAD96620.1; -; mRNA.
DR EMBL; AF177344; AAG17988.2; -; mRNA.
DR EMBL; CH471108; EAW90642.1; -; Genomic_DNA.
DR EMBL; BC011550; AAH11550.1; -; mRNA.
DR EMBL; BC050614; AAH50614.1; -; mRNA.
DR CCDS; CCDS10997.1; -.
DR RefSeq; NP_001304876.1; NM_001317947.1.
DR RefSeq; NP_060616.1; NM_018146.3.
DR PDB; 7OI6; EM; 5.70 A; 1/z=1-420.
DR PDBsum; 7OI6; -.
DR AlphaFoldDB; Q9HC36; -.
DR SMR; Q9HC36; -.
DR BioGRID; 120477; 164.
DR IntAct; Q9HC36; 67.
DR MINT; Q9HC36; -.
DR STRING; 9606.ENSP00000306080; -.
DR GlyGen; Q9HC36; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q9HC36; -.
DR PhosphoSitePlus; Q9HC36; -.
DR BioMuta; MRM3; -.
DR DMDM; 74734265; -.
DR EPD; Q9HC36; -.
DR jPOST; Q9HC36; -.
DR MassIVE; Q9HC36; -.
DR MaxQB; Q9HC36; -.
DR PaxDb; Q9HC36; -.
DR PeptideAtlas; Q9HC36; -.
DR PRIDE; Q9HC36; -.
DR ProteomicsDB; 81632; -.
DR Antibodypedia; 10311; 108 antibodies from 21 providers.
DR DNASU; 55178; -.
DR Ensembl; ENST00000304478.9; ENSP00000306080.4; ENSG00000171861.11.
DR GeneID; 55178; -.
DR KEGG; hsa:55178; -.
DR MANE-Select; ENST00000304478.9; ENSP00000306080.4; NM_018146.4; NP_060616.1.
DR UCSC; uc002frw.4; human.
DR CTD; 55178; -.
DR GeneCards; MRM3; -.
DR HGNC; HGNC:18485; MRM3.
DR HPA; ENSG00000171861; Low tissue specificity.
DR MIM; 612600; gene.
DR neXtProt; NX_Q9HC36; -.
DR OpenTargets; ENSG00000171861; -.
DR PharmGKB; PA38341; -.
DR VEuPathDB; HostDB:ENSG00000171861; -.
DR eggNOG; KOG2506; Eukaryota.
DR GeneTree; ENSGT00390000017317; -.
DR HOGENOM; CLU_021322_1_0_1; -.
DR InParanoid; Q9HC36; -.
DR OMA; ERKRAPG; -.
DR OrthoDB; 1183644at2759; -.
DR PhylomeDB; Q9HC36; -.
DR TreeFam; TF323420; -.
DR BRENDA; 2.1.1.B124; 2681.
DR PathwayCommons; Q9HC36; -.
DR Reactome; R-HSA-6793080; rRNA modification in the mitochondrion.
DR SignaLink; Q9HC36; -.
DR BioGRID-ORCS; 55178; 101 hits in 1079 CRISPR screens.
DR ChiTaRS; MRM3; human.
DR GeneWiki; RNMTL1; -.
DR GenomeRNAi; 55178; -.
DR Pharos; Q9HC36; Tbio.
DR PRO; PR:Q9HC36; -.
DR Proteomes; UP000005640; Chromosome 17.
DR RNAct; Q9HC36; protein.
DR Bgee; ENSG00000171861; Expressed in endothelial cell and 185 other tissues.
DR ExpressionAtlas; Q9HC36; baseline and differential.
DR Genevisible; Q9HC36; HS.
DR GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
DR GO; GO:0005739; C:mitochondrion; IDA:HPA.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0070039; F:rRNA (guanosine-2'-O-)-methyltransferase activity; IMP:FlyBase.
DR GO; GO:0000451; P:rRNA 2'-O-methylation; TAS:Reactome.
DR Gene3D; 3.30.1330.30; -; 1.
DR Gene3D; 3.40.1280.10; -; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR029064; L30e-like.
DR InterPro; IPR001537; SpoU_MeTrfase.
DR InterPro; IPR013123; SpoU_subst-bd.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR Pfam; PF00588; SpoU_methylase; 1.
DR SMART; SM00967; SpoU_sub_bind; 1.
DR SUPFAM; SSF55315; SSF55315; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Mitochondrion; Reference proteome;
KW rRNA processing; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT TRANSIT 1..40
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 41..420
FT /note="rRNA methyltransferase 3, mitochondrial"
FT /id="PRO_0000311301"
FT REGION 49..88
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 356
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 380
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 389
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT VARIANT 8
FT /note="A -> S (in dbSNP:rs2273454)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_037217"
FT VARIANT 45
FT /note="G -> E (in dbSNP:rs2249542)"
FT /id="VAR_037218"
FT VARIANT 185
FT /note="I -> V (in dbSNP:rs17854653)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_037219"
FT VARIANT 326
FT /note="E -> Q (in dbSNP:rs35780267)"
FT /id="VAR_037220"
FT CONFLICT 247
FT /note="A -> V (in Ref. 3; BAD96620)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 420 AA; 47020 MW; CC06C27489A89FC3 CRC64;
MAALVRPARF VVRPLLQVVQ AWDLDARRWV RALRRSPVKV VFPSGEVVEQ KRAPGKQPRK
APSEASAQEQ REKQPLEESA SRAPSTWEES GLRYDKAYPG DRRLSSVMTI VKSRPFREKQ
GKILLEGRRL ISDALKAGAV PKMFFFSRLE YLKELPVDKL KGVSLIKVKF EDIKDWSDLV
TPQGIMGIFA KPDHVKMTYP KTQLQHSLPL LLICDNLRDP GNLGTILRSA AGAGCSKVLL
TKGCVDAWEP KVLRAGMGAH FRMPIINNLE WETVPNYLPP DTRVYVADNC GLYAQAEMSN
KASDHGWVCD QRVMKFHKYE EEEDVETGAS QDWLPHVEVQ SYDSDWTEAP AAVVIGGETY
GVSLESLQLA ESTGGKRLLI PVVPGVDSLN SAMAASILLF EGKRQLRGRA EDLSRDRSYH
