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Protein

rRNA methyltransferase 3, mitochondrial

Gene

RNMTL1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O-methylguanosine at position 1370 (Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA.3 Publications

Catalytic activityi

S-adenosyl-L-methionine + guanosine(1370) in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(1370) in 16S rRNA.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei356 – 3561S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei380 – 3801S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei389 – 3891S-adenosyl-L-methionine; via amide nitrogenBy similarity

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB
  2. RNA methyltransferase activity Source: InterPro

GO - Biological processi

  1. RNA processing Source: InterPro
  2. rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
rRNA methyltransferase 3, mitochondrial1 Publication (EC:2.1.1.-2 Publications)
Alternative name(s):
16S rRNA (guanosine(1370)-2'-O)-methyltransferase1 Publication
16S rRNA [Gm1370] 2'-O-methyltransferase1 Publication
RNA methyltransferase-like protein 11 Publication
Gene namesi
Name:RNMTL11 Publication
Synonyms:MRM31 Publication
ORF Names:HC90
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:18485. RNMTL1.

Subcellular locationi

  1. Mitochondrion 2 Publications

GO - Cellular componenti

  1. mitochondrion Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA38341.

Polymorphism and mutation databases

BioMutaiRNMTL1.
DMDMi74734265.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4040MitochondrionSequence AnalysisAdd
BLAST
Chaini41 – 420380rRNA methyltransferase 3, mitochondrialPRO_0000311301Add
BLAST

Proteomic databases

MaxQBiQ9HC36.
PaxDbiQ9HC36.
PRIDEiQ9HC36.

PTM databases

PhosphoSiteiQ9HC36.

Expressioni

Tissue specificityi

Expressed at same level in normal liver and hepatocarcinoma.1 Publication

Gene expression databases

BgeeiQ9HC36.
CleanExiHS_RNMTL1.
ExpressionAtlasiQ9HC36. baseline and differential.
GenevestigatoriQ9HC36.

Organism-specific databases

HPAiHPA022534.
HPA023031.
HPA023292.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
FHL3Q136433EBI-1045440,EBI-741101

Protein-protein interaction databases

BioGridi120477. 33 interactions.
IntActiQ9HC36. 3 interactions.
MINTiMINT-8052394.
STRINGi9606.ENSP00000306080.

Structurei

3D structure databases

ProteinModelPortaliQ9HC36.
SMRiQ9HC36. Positions 103-405.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0566.
GeneTreeiENSGT00390000017317.
HOGENOMiHOG000154151.
HOVERGENiHBG108411.
InParanoidiQ9HC36.
OMAiRYDKAFP.
OrthoDBiEOG7MSMPJ.
PhylomeDBiQ9HC36.
TreeFamiTF323420.

Family and domain databases

Gene3Di3.30.1330.30. 1 hit.
3.40.1280.10. 2 hits.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR029064. L30e-like.
IPR001537. SpoU_MeTrfase.
IPR013123. SpoU_subst-bd.
IPR029026. tRNA_m1G_MTases_N.
[Graphical view]
PfamiPF00588. SpoU_methylase. 1 hit.
PF08032. SpoU_sub_bind. 1 hit.
[Graphical view]
SMARTiSM00967. SpoU_sub_bind. 1 hit.
[Graphical view]
SUPFAMiSSF55315. SSF55315. 1 hit.
SSF75217. SSF75217. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9HC36-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAALVRPARF VVRPLLQVVQ AWDLDARRWV RALRRSPVKV VFPSGEVVEQ
60 70 80 90 100
KRAPGKQPRK APSEASAQEQ REKQPLEESA SRAPSTWEES GLRYDKAYPG
110 120 130 140 150
DRRLSSVMTI VKSRPFREKQ GKILLEGRRL ISDALKAGAV PKMFFFSRLE
160 170 180 190 200
YLKELPVDKL KGVSLIKVKF EDIKDWSDLV TPQGIMGIFA KPDHVKMTYP
210 220 230 240 250
KTQLQHSLPL LLICDNLRDP GNLGTILRSA AGAGCSKVLL TKGCVDAWEP
260 270 280 290 300
KVLRAGMGAH FRMPIINNLE WETVPNYLPP DTRVYVADNC GLYAQAEMSN
310 320 330 340 350
KASDHGWVCD QRVMKFHKYE EEEDVETGAS QDWLPHVEVQ SYDSDWTEAP
360 370 380 390 400
AAVVIGGETY GVSLESLQLA ESTGGKRLLI PVVPGVDSLN SAMAASILLF
410 420
EGKRQLRGRA EDLSRDRSYH
Length:420
Mass (Da):47,020
Last modified:June 1, 2002 - v2
Checksum:iCC06C27489A89FC3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti247 – 2471A → V in BAD96620 (Ref. 3) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti8 – 81A → S.1 Publication
Corresponds to variant rs2273454 [ dbSNP | Ensembl ].
VAR_037217
Natural varianti45 – 451G → E.
Corresponds to variant rs2249542 [ dbSNP | Ensembl ].
VAR_037218
Natural varianti185 – 1851I → V.1 Publication
Corresponds to variant rs17854653 [ dbSNP | Ensembl ].
VAR_037219
Natural varianti326 – 3261E → Q.
Corresponds to variant rs35780267 [ dbSNP | Ensembl ].
VAR_037220

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001443 mRNA. Translation: BAA91694.1.
AK222900 mRNA. Translation: BAD96620.1.
AF177344 mRNA. Translation: AAG17988.2.
CH471108 Genomic DNA. Translation: EAW90642.1.
BC011550 mRNA. Translation: AAH11550.1.
BC050614 mRNA. Translation: AAH50614.1.
CCDSiCCDS10997.1.
RefSeqiNP_060616.1. NM_018146.2.
UniGeneiHs.182729.

Genome annotation databases

EnsembliENST00000304478; ENSP00000306080; ENSG00000171861.
GeneIDi55178.
KEGGihsa:55178.
UCSCiuc002frw.3. human.

Polymorphism and mutation databases

BioMutaiRNMTL1.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001443 mRNA. Translation: BAA91694.1.
AK222900 mRNA. Translation: BAD96620.1.
AF177344 mRNA. Translation: AAG17988.2.
CH471108 Genomic DNA. Translation: EAW90642.1.
BC011550 mRNA. Translation: AAH11550.1.
BC050614 mRNA. Translation: AAH50614.1.
CCDSiCCDS10997.1.
RefSeqiNP_060616.1. NM_018146.2.
UniGeneiHs.182729.

3D structure databases

ProteinModelPortaliQ9HC36.
SMRiQ9HC36. Positions 103-405.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120477. 33 interactions.
IntActiQ9HC36. 3 interactions.
MINTiMINT-8052394.
STRINGi9606.ENSP00000306080.

PTM databases

PhosphoSiteiQ9HC36.

Polymorphism and mutation databases

BioMutaiRNMTL1.
DMDMi74734265.

Proteomic databases

MaxQBiQ9HC36.
PaxDbiQ9HC36.
PRIDEiQ9HC36.

Protocols and materials databases

DNASUi55178.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000304478; ENSP00000306080; ENSG00000171861.
GeneIDi55178.
KEGGihsa:55178.
UCSCiuc002frw.3. human.

Organism-specific databases

CTDi55178.
GeneCardsiGC17P000685.
HGNCiHGNC:18485. RNMTL1.
HPAiHPA022534.
HPA023031.
HPA023292.
MIMi612600. gene.
neXtProtiNX_Q9HC36.
PharmGKBiPA38341.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0566.
GeneTreeiENSGT00390000017317.
HOGENOMiHOG000154151.
HOVERGENiHBG108411.
InParanoidiQ9HC36.
OMAiRYDKAFP.
OrthoDBiEOG7MSMPJ.
PhylomeDBiQ9HC36.
TreeFamiTF323420.

Miscellaneous databases

ChiTaRSiRNMTL1. human.
GeneWikiiRNMTL1.
GenomeRNAii55178.
NextBioi58983.
PROiQ9HC36.
SOURCEiSearch...

Gene expression databases

BgeeiQ9HC36.
CleanExiHS_RNMTL1.
ExpressionAtlasiQ9HC36. baseline and differential.
GenevestigatoriQ9HC36.

Family and domain databases

Gene3Di3.30.1330.30. 1 hit.
3.40.1280.10. 2 hits.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR029064. L30e-like.
IPR001537. SpoU_MeTrfase.
IPR013123. SpoU_subst-bd.
IPR029026. tRNA_m1G_MTases_N.
[Graphical view]
PfamiPF00588. SpoU_methylase. 1 hit.
PF08032. SpoU_sub_bind. 1 hit.
[Graphical view]
SMARTiSM00967. SpoU_sub_bind. 1 hit.
[Graphical view]
SUPFAMiSSF55315. SSF55315. 1 hit.
SSF75217. SSF75217. 2 hits.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Teratocarcinoma.
  2. Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.
  3. "Homo sapiens P579 chromosome 17p DNA sequence fragment."
    Gu J.R., Zhao X.T., Wan D.F., Jiang H.Q., Huang Y., He Y.H., Qin W.X., Han L.W., Zhang P.P., Qiu X.K., He L.P.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS SER-8 AND VAL-185.
    Tissue: Brain and Skin.
  6. "The ATF/CREB site is the key element for transcription of the human RNA methyltransferase like 1(RNMTL1) gene, a newly discovered 17p13.3 gene."
    Xu J., De Zhu J., Ni M., Wan F., Gu J.R.
    Cell Res. 12:177-197(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid."
    Lee K.W., Okot-Kotber C., LaComb J.F., Bogenhagen D.F.
    J. Biol. Chem. 288:31386-31399(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  9. "Assignment of 2'-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16S rRNA."
    Lee K.W., Bogenhagen D.F.
    J. Biol. Chem. 289:24936-24942(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  11. "MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome."
    Rorbach J., Boesch P., Gammage P.A., Nicholls T.J., Pearce S.F., Patel D., Hauser A., Perocchi F., Minczuk M.
    Mol. Biol. Cell 25:2542-2555(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiMRM3_HUMAN
AccessioniPrimary (citable) accession number: Q9HC36
Secondary accession number(s): Q53GN1
, Q86VC3, Q96F76, Q9NVQ5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: June 1, 2002
Last modified: April 29, 2015
This is version 106 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.