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Protein

tRNA (cytosine(38)-C(5))-methyltransferase

Gene

TRDMT1

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

Functioni

Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp).1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cytosine(38) in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(38) in tRNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei79PROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:HS03011-MONOMER.
ZFISH:HS03011-MONOMER.
BRENDAi2.1.1.204. 2681.
ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (cytosine(38)-C(5))-methyltransferase (EC:2.1.1.204)
Alternative name(s):
DNA (cytosine-5)-methyltransferase-like protein 2
Short name:
Dnmt2
DNA methyltransferase homolog HsaIIP
Short name:
DNA MTase homolog HsaIIP
Short name:
M.HsaIIP
PuMet
Gene namesi
Name:TRDMT1
Synonyms:DNMT2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:2977. TRDMT1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi1787.
OpenTargetsiENSG00000107614.
PharmGKBiPA162406922.

Chemistry databases

DrugBankiDB00738. Pentamidine.

Polymorphism and mutation databases

BioMutaiTRDMT1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000880401 – 391tRNA (cytosine(38)-C(5))-methyltransferaseAdd BLAST391

Proteomic databases

PaxDbiO14717.
PeptideAtlasiO14717.
PRIDEiO14717.

PTM databases

iPTMnetiO14717.
PhosphoSitePlusiO14717.

Expressioni

Tissue specificityi

Ubiquitous. Higher expression in testis, ovary and thymus and at much lower levels in spleen, prostate, colon, small intestine, and peripheral blood leukocytes.

Gene expression databases

BgeeiENSG00000107614.
CleanExiHS_TRDMT1.
ExpressionAtlasiO14717. baseline and differential.
GenevisibleiO14717. HS.

Organism-specific databases

HPAiCAB009468.
HPA036945.
HPA036946.

Interactioni

Protein-protein interaction databases

BioGridi108124. 14 interactors.
IntActiO14717. 13 interactors.
STRINGi9606.ENSP00000367030.

Structurei

Secondary structure

1391
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Helixi15 – 23Combined sources9
Beta strandi26 – 33Combined sources8
Helixi37 – 46Combined sources10
Helixi57 – 59Combined sources3
Helixi62 – 68Combined sources7
Beta strandi71 – 75Combined sources5
Helixi98 – 105Combined sources8
Helixi106 – 108Combined sources3
Beta strandi114 – 121Combined sources8
Helixi124 – 126Combined sources3
Helixi128 – 139Combined sources12
Beta strandi142 – 149Combined sources8
Helixi151 – 154Combined sources4
Beta strandi162 – 172Combined sources11
Beta strandi182 – 185Combined sources4
Helixi253 – 256Combined sources4
Helixi263 – 266Combined sources4
Helixi270 – 276Combined sources7
Helixi277 – 279Combined sources3
Turni295 – 299Combined sources5
Beta strandi307 – 309Combined sources3
Helixi316 – 321Combined sources6
Turni322 – 325Combined sources4
Helixi328 – 336Combined sources9
Helixi345 – 351Combined sources7
Helixi366 – 375Combined sources10
Helixi379 – 390Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G55X-ray1.80A2-391[»]
ProteinModelPortaliO14717.
SMRiO14717.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO14717.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini4 – 391SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd BLAST388

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation
Contains 1 SAM-dependent MTase C5-type domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0919. Eukaryota.
COG0270. LUCA.
GeneTreeiENSGT00390000016416.
HOVERGENiHBG051385.
InParanoidiO14717.
KOiK15336.
OMAiQSFDINT.
OrthoDBiEOG091G0FXV.
PhylomeDBiO14717.
TreeFamiTF300024.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001525. C5_MeTfrase.
IPR031303. C5_meth_CS.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF00145. DNA_methylase. 1 hit.
[Graphical view]
PRINTSiPR00105. C5METTRFRASE.
SUPFAMiSSF53335. SSF53335. 2 hits.
TIGRFAMsiTIGR00675. dcm. 1 hit.
PROSITEiPS00095. C5_MTASE_2. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform A (identifier: O14717-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEPLRVLELY SGVGGMHHAL RESCIPAQVV AAIDVNTVAN EVYKYNFPHT
60 70 80 90 100
QLLAKTIEGI TLEEFDRLSF DMILMSPPCQ PFTRIGRQGD MTDSRTNSFL
110 120 130 140 150
HILDILPRLQ KLPKYILLEN VKGFEVSSTR DLLIQTIENC GFQYQEFLLS
160 170 180 190 200
PTSLGIPNSR LRYFLIAKLQ SEPLPFQAPG QVLMEFPKIE SVHPQKYAMD
210 220 230 240 250
VENKIQEKNV EPNISFDGSI QCSGKDAILF KLETAEEIHR KNQQDSDLSV
260 270 280 290 300
KMLKDFLEDD TDVNQYLLPP KSLLRYALLL DIVQPTCRRS VCFTKGYGSY
310 320 330 340 350
IEGTGSVLQT AEDVQVENIY KSLTNLSQEE QITKLLILKL RYFTPKEIAN
360 370 380 390
LLGFPPEFGF PEKITVKQRY RLLGNSLNVH VVAKLIKILY E
Length:391
Mass (Da):44,597
Last modified:January 1, 1998 - v1
Checksum:iBCA549E4EB2E6950
GO
Isoform B (identifier: O14717-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     84-107: Missing.

Show »
Length:367
Mass (Da):41,858
Checksum:i3801D5651DBC2614
GO
Isoform C (identifier: O14717-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     84-129: Missing.

Show »
Length:345
Mass (Da):39,313
Checksum:i65939D1BE01D958B
GO
Isoform D (identifier: O14717-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     59-63: GITLE → DWPAG
     64-391: Missing.

Show »
Length:63
Mass (Da):6,965
Checksum:i3DBEA06674461233
GO
Isoform E (identifier: O14717-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     59-71: GITLEEFDRLSFD → ITKITKVYSFGKC
     72-391: Missing.

Show »
Length:71
Mass (Da):7,908
Checksum:i862BC392F37BFA8C
GO
Isoform F (identifier: O14717-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     59-107: GITLEEFDRL...SFLHILDILP → RPLDTNNRKL...SVRAITLSSP
     108-391: Missing.

Show »
Length:107
Mass (Da):12,087
Checksum:iBDD5DD4DC6D6BD3E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti148L → I in AAC39764 (PubMed:9592134).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051961101H → Y.1 PublicationCorresponds to variant rs11254413dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00563459 – 107GITLE…LDILP → RPLDTNNRKLWLSVPRVYII SNLSWHSKFKATIFSYCKAS VRAITLSSP in isoform F. 1 PublicationAdd BLAST49
Alternative sequenceiVSP_00563259 – 71GITLE…RLSFD → ITKITKVYSFGKC in isoform E. 1 PublicationAdd BLAST13
Alternative sequenceiVSP_00563059 – 63GITLE → DWPAG in isoform D. 1 Publication5
Alternative sequenceiVSP_00563164 – 391Missing in isoform D. 1 PublicationAdd BLAST328
Alternative sequenceiVSP_00563372 – 391Missing in isoform E. 1 PublicationAdd BLAST320
Alternative sequenceiVSP_00562984 – 129Missing in isoform C. 1 PublicationAdd BLAST46
Alternative sequenceiVSP_00562884 – 107Missing in isoform B. 1 PublicationAdd BLAST24
Alternative sequenceiVSP_005635108 – 391Missing in isoform F. 1 PublicationAdd BLAST284

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012128 mRNA. Translation: AAC51939.1.
AJ223333 mRNA. Translation: CAA11272.1.
AF045888 mRNA. Translation: AAC39764.1.
EF444974 Genomic DNA. Translation: ACA05980.1.
EF444974 Genomic DNA. Translation: ACA05984.1.
EF444974 Genomic DNA. Translation: ACA05985.1.
EF444974 Genomic DNA. Translation: ACA05986.1.
AL133415, AC067747 Genomic DNA. Translation: CAB87964.1.
CH471072 Genomic DNA. Translation: EAW86218.1.
CH471072 Genomic DNA. Translation: EAW86219.1.
BC047733 mRNA. Translation: AAH47733.1.
AF329940 mRNA. Translation: AAK68034.1.
AF329941 mRNA. Translation: AAK68035.1.
AF329942 mRNA. Translation: AAK68036.1.
AF329943 mRNA. Translation: AAK68037.1.
AF329944 mRNA. Translation: AAK68033.1.
CCDSiCCDS7114.1. [O14717-1]
RefSeqiNP_001307935.1. NM_001321006.1.
NP_001307936.1. NM_001321007.1.
NP_004403.1. NM_004412.6. [O14717-1]
XP_005252432.1. XM_005252375.4. [O14717-3]
UniGeneiHs.351665.
Hs.564140.

Genome annotation databases

EnsembliENST00000377799; ENSP00000367030; ENSG00000107614. [O14717-1]
ENST00000495022; ENSP00000417594; ENSG00000107614. [O14717-4]
GeneIDi1787.
KEGGihsa:1787.
UCSCiuc057sar.1. human. [O14717-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF012128 mRNA. Translation: AAC51939.1.
AJ223333 mRNA. Translation: CAA11272.1.
AF045888 mRNA. Translation: AAC39764.1.
EF444974 Genomic DNA. Translation: ACA05980.1.
EF444974 Genomic DNA. Translation: ACA05984.1.
EF444974 Genomic DNA. Translation: ACA05985.1.
EF444974 Genomic DNA. Translation: ACA05986.1.
AL133415, AC067747 Genomic DNA. Translation: CAB87964.1.
CH471072 Genomic DNA. Translation: EAW86218.1.
CH471072 Genomic DNA. Translation: EAW86219.1.
BC047733 mRNA. Translation: AAH47733.1.
AF329940 mRNA. Translation: AAK68034.1.
AF329941 mRNA. Translation: AAK68035.1.
AF329942 mRNA. Translation: AAK68036.1.
AF329943 mRNA. Translation: AAK68037.1.
AF329944 mRNA. Translation: AAK68033.1.
CCDSiCCDS7114.1. [O14717-1]
RefSeqiNP_001307935.1. NM_001321006.1.
NP_001307936.1. NM_001321007.1.
NP_004403.1. NM_004412.6. [O14717-1]
XP_005252432.1. XM_005252375.4. [O14717-3]
UniGeneiHs.351665.
Hs.564140.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G55X-ray1.80A2-391[»]
ProteinModelPortaliO14717.
SMRiO14717.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi108124. 14 interactors.
IntActiO14717. 13 interactors.
STRINGi9606.ENSP00000367030.

Chemistry databases

DrugBankiDB00738. Pentamidine.

PTM databases

iPTMnetiO14717.
PhosphoSitePlusiO14717.

Polymorphism and mutation databases

BioMutaiTRDMT1.

Proteomic databases

PaxDbiO14717.
PeptideAtlasiO14717.
PRIDEiO14717.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000377799; ENSP00000367030; ENSG00000107614. [O14717-1]
ENST00000495022; ENSP00000417594; ENSG00000107614. [O14717-4]
GeneIDi1787.
KEGGihsa:1787.
UCSCiuc057sar.1. human. [O14717-1]

Organism-specific databases

CTDi1787.
DisGeNETi1787.
GeneCardsiTRDMT1.
HGNCiHGNC:2977. TRDMT1.
HPAiCAB009468.
HPA036945.
HPA036946.
MIMi602478. gene.
neXtProtiNX_O14717.
OpenTargetsiENSG00000107614.
PharmGKBiPA162406922.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0919. Eukaryota.
COG0270. LUCA.
GeneTreeiENSGT00390000016416.
HOVERGENiHBG051385.
InParanoidiO14717.
KOiK15336.
OMAiQSFDINT.
OrthoDBiEOG091G0FXV.
PhylomeDBiO14717.
TreeFamiTF300024.

Enzyme and pathway databases

BioCyciMetaCyc:HS03011-MONOMER.
ZFISH:HS03011-MONOMER.
BRENDAi2.1.1.204. 2681.
ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

ChiTaRSiTRDMT1. human.
EvolutionaryTraceiO14717.
GeneWikiiTRDMT1.
GenomeRNAii1787.
PROiO14717.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000107614.
CleanExiHS_TRDMT1.
ExpressionAtlasiO14717. baseline and differential.
GenevisibleiO14717. HS.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001525. C5_MeTfrase.
IPR031303. C5_meth_CS.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF00145. DNA_methylase. 1 hit.
[Graphical view]
PRINTSiPR00105. C5METTRFRASE.
SUPFAMiSSF53335. SSF53335. 2 hits.
TIGRFAMsiTIGR00675. dcm. 1 hit.
PROSITEiPS00095. C5_MTASE_2. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTRDMT_HUMAN
AccessioniPrimary (citable) accession number: O14717
Secondary accession number(s): B0YJ02
, B0YJ03, B0YJ07, B0YJ08, O43669, Q86WW6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 145 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 10
    Human chromosome 10: 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.