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Protein

tRNA methyltransferase 10 homolog A

Gene

TRMT10A

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

Functioni

RNA methyltransferase.1 Publication

GO - Molecular functioni

  • methyltransferase activity Source: UniProtKB-KW
  • poly(A) RNA binding Source: UniProtKB
  • tRNA binding Source: UniProtKB

GO - Biological processi

  • tRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA methyltransferase 10 homolog A (EC:2.1.1.-)
Alternative name(s):
RNA (guanine-9-)-methyltransferase domain-containing protein 2
Gene namesi
Name:TRMT10A
Synonyms:RG9MTD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:28403. TRMT10A.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Microcephaly, short stature, and impaired glucose metabolism 1 (MSSGM1)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disease characterized by microcephaly, mental retardation, short stature, and disturbed glucose metabolism. Additional clinical features include delayed puberty, hypoglycemia-related seizures, hyperinsulinemic hypoglycemia, and early-onset diabetes.
See also OMIM:616033
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti206 – 2061G → R in MSSGM1; results in loss of activity; does not affect affinity for Gly-tRNA. 1 Publication
VAR_072420

Keywords - Diseasei

Diabetes mellitus, Disease mutation, Dwarfism, Mental retardation

Organism-specific databases

MalaCardsiTRMT10A.
MIMi616033. phenotype.
Orphaneti391408. Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome.
PharmGKBiPA134979919.

Polymorphism and mutation databases

BioMutaiTRMT10A.
DMDMi74730533.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 339339tRNA methyltransferase 10 homolog APRO_0000311315Add
BLAST

Proteomic databases

EPDiQ8TBZ6.
PaxDbiQ8TBZ6.
PRIDEiQ8TBZ6.

PTM databases

iPTMnetiQ8TBZ6.
PhosphoSiteiQ8TBZ6.

Expressioni

Tissue specificityi

Expressed in embryonic and fetal brain. It is expressed throughout the dorsal telencephalon at 8 and 11 weeks of gestation, with highest expression in ventricular zone and marginal zone. Detected in cerebellar cortex and nuclei, but not in dorsal telencephalon, at later stages.1 Publication

Gene expression databases

BgeeiQ8TBZ6.
CleanExiHS_RG9MTD2.
ExpressionAtlasiQ8TBZ6. baseline and differential.
GenevisibleiQ8TBZ6. HS.

Organism-specific databases

HPAiHPA047601.

Interactioni

Subunit structurei

Interacts with tRNA.1 Publication

Protein-protein interaction databases

BioGridi125035. 13 interactions.
IntActiQ8TBZ6. 4 interactions.
STRINGi9606.ENSP00000273962.

Structurei

Secondary structure

1
339
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi102 – 1065Combined sources
Helixi110 – 1123Combined sources
Helixi115 – 13420Combined sources
Beta strandi140 – 1456Combined sources
Helixi148 – 15710Combined sources
Helixi159 – 1624Combined sources
Helixi174 – 1774Combined sources
Helixi180 – 1823Combined sources
Beta strandi183 – 1864Combined sources
Beta strandi201 – 2066Combined sources
Helixi217 – 2259Combined sources
Beta strandi228 – 2314Combined sources
Turni235 – 2373Combined sources
Helixi248 – 26114Combined sources
Helixi264 – 2718Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FMWX-ray2.00A/B82-277[»]
ProteinModelPortaliQ8TBZ6.
SMRiQ8TBZ6. Positions 94-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini89 – 279191SAM-dependent MTase TRM10-typePROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili52 – 8130Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.PROSITE-ProRule annotation
Contains 1 SAM-dependent MTase TRM10-type domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2967. Eukaryota.
ENOG4111JE4. LUCA.
HOGENOMiHOG000195825.
HOVERGENiHBG108403.
InParanoidiQ8TBZ6.
KOiK15445.
OMAiCESASHD.
OrthoDBiEOG7QC7X8.
PhylomeDBiQ8TBZ6.
TreeFamiTF330972.

Family and domain databases

InterProiIPR028564. MT_TRM10-typ.
IPR007356. tRNA_m1G_MeTrfase_euk.
IPR016653. tRNA_MeTfrase_TRM10.
IPR016009. tRNA_MeTrfase_TRMD/TRM10.
[Graphical view]
PANTHERiPTHR13563. PTHR13563. 1 hit.
PfamiPF01746. tRNA_m1G_MT. 1 hit.
[Graphical view]
PIRSFiPIRSF016323. tRNA_m1G_mtfrase_met. 1 hit.
PROSITEiPS51675. SAM_MT_TRM10. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8TBZ6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSEMLPAFI ETSNVDKKQG INEDQEESQK PRLGEGCEPI SKRQMKKLIK
60 70 80 90 100
QKQWEEQREL RKQKRKEKRK RKKLERQCQM EPNSDGHDRK RVRRDVVHST
110 120 130 140 150
LRLIIDCSFD HLMVLKDIKK LHKQIQRCYA ENRRALHPVQ FYLTSHGGQL
160 170 180 190 200
KKNMDENDKG WVNWKDIHIK PEHYSELIKK EDLIYLTSDS PNILKELDES
210 220 230 240 250
KAYVIGGLVD HNHHKGLTYK QASDYGINHA QLPLGNFVKM NSRKVLAVNH
260 270 280 290 300
VFEIILEYLE TRDWQEAFFT ILPQRKGAVP TDKACESASH DNQSVRMEEG
310 320 330
GSDSDSSEEE YSRNELDSPH EEKQDKENHT ESTVNSLPH
Length:339
Mass (Da):39,719
Last modified:June 1, 2002 - v1
Checksum:i1FCDA258DD7CA04D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti292 – 2921N → F in AAD21019 (Ref. 4) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti82 – 821P → Q in a breast cancer sample; somatic mutation. 1 Publication
VAR_037222
Natural varianti133 – 1331R → Q.
Corresponds to variant rs10007569 [ dbSNP | Ensembl ].
VAR_037223
Natural varianti206 – 2061G → R in MSSGM1; results in loss of activity; does not affect affinity for Gly-tRNA. 1 Publication
VAR_072420

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK313548 mRNA. Translation: BAG36324.1.
CH471057 Genomic DNA. Translation: EAX06104.1.
BC028373 mRNA. Translation: AAH28373.1.
AF106046 mRNA. Translation: AAD21019.1.
CCDSiCCDS3650.1.
RefSeqiNP_001128137.1. NM_001134665.2.
NP_001128138.1. NM_001134666.2.
NP_689505.1. NM_152292.4.
XP_005263409.1. XM_005263352.3.
XP_006714480.1. XM_006714417.2.
UniGeneiHs.380412.

Genome annotation databases

EnsembliENST00000273962; ENSP00000273962; ENSG00000145331.
ENST00000394876; ENSP00000378342; ENSG00000145331.
ENST00000394877; ENSP00000378343; ENSG00000145331.
GeneIDi93587.
KEGGihsa:93587.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK313548 mRNA. Translation: BAG36324.1.
CH471057 Genomic DNA. Translation: EAX06104.1.
BC028373 mRNA. Translation: AAH28373.1.
AF106046 mRNA. Translation: AAD21019.1.
CCDSiCCDS3650.1.
RefSeqiNP_001128137.1. NM_001134665.2.
NP_001128138.1. NM_001134666.2.
NP_689505.1. NM_152292.4.
XP_005263409.1. XM_005263352.3.
XP_006714480.1. XM_006714417.2.
UniGeneiHs.380412.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FMWX-ray2.00A/B82-277[»]
ProteinModelPortaliQ8TBZ6.
SMRiQ8TBZ6. Positions 94-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125035. 13 interactions.
IntActiQ8TBZ6. 4 interactions.
STRINGi9606.ENSP00000273962.

PTM databases

iPTMnetiQ8TBZ6.
PhosphoSiteiQ8TBZ6.

Polymorphism and mutation databases

BioMutaiTRMT10A.
DMDMi74730533.

Proteomic databases

EPDiQ8TBZ6.
PaxDbiQ8TBZ6.
PRIDEiQ8TBZ6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000273962; ENSP00000273962; ENSG00000145331.
ENST00000394876; ENSP00000378342; ENSG00000145331.
ENST00000394877; ENSP00000378343; ENSG00000145331.
GeneIDi93587.
KEGGihsa:93587.

Organism-specific databases

CTDi93587.
GeneCardsiTRMT10A.
H-InvDBHIX0004399.
HGNCiHGNC:28403. TRMT10A.
HPAiHPA047601.
MalaCardsiTRMT10A.
MIMi616013. gene.
616033. phenotype.
neXtProtiNX_Q8TBZ6.
Orphaneti391408. Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome.
PharmGKBiPA134979919.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2967. Eukaryota.
ENOG4111JE4. LUCA.
HOGENOMiHOG000195825.
HOVERGENiHBG108403.
InParanoidiQ8TBZ6.
KOiK15445.
OMAiCESASHD.
OrthoDBiEOG7QC7X8.
PhylomeDBiQ8TBZ6.
TreeFamiTF330972.

Enzyme and pathway databases

ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

GenomeRNAii93587.
PROiQ8TBZ6.
SOURCEiSearch...

Gene expression databases

BgeeiQ8TBZ6.
CleanExiHS_RG9MTD2.
ExpressionAtlasiQ8TBZ6. baseline and differential.
GenevisibleiQ8TBZ6. HS.

Family and domain databases

InterProiIPR028564. MT_TRM10-typ.
IPR007356. tRNA_m1G_MeTrfase_euk.
IPR016653. tRNA_MeTfrase_TRM10.
IPR016009. tRNA_MeTrfase_TRMD/TRM10.
[Graphical view]
PANTHERiPTHR13563. PTHR13563. 1 hit.
PfamiPF01746. tRNA_m1G_MT. 1 hit.
[Graphical view]
PIRSFiPIRSF016323. tRNA_m1G_mtfrase_met. 1 hit.
PROSITEiPS51675. SAM_MT_TRM10. 1 hit.
[Graphical view]
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].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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].
    Tissue: Testis.
  4. "Homo sapiens cDNA clone 44 from HTLV-1 transformed lymphocyte library."
    Ji Y., Huang T., Johnson B.H., Thompson E.B.
    Submitted (NOV-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 107-339.
  5. Cited for: INVOLVEMENT IN MSSGM1, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  6. "TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly."
    Gillis D., Krishnamohan A., Yaacov B., Shaag A., Jackman J.E., Elpeleg O.
    J. Med. Genet. 51:581-586(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH TRANSFER RNA, INVOLVEMENT IN MSSGM1, VARIANT MSSGM1 ARG-206, CHARACTERIZATION OF VARIANT MSSGM1 ARG-206.
  7. Cited for: VARIANT [LARGE SCALE ANALYSIS] GLN-82.

Entry informationi

Entry nameiTM10A_HUMAN
AccessioniPrimary (citable) accession number: Q8TBZ6
Secondary accession number(s): B2R8X7, Q9Y2T9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: June 1, 2002
Last modified: June 8, 2016
This is version 107 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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 one 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.