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Protein

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

Gene

TRDMT1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
Binding sitei34S-adenosyl-L-methionineCombined sources1 Publication1
Binding sitei76S-adenosyl-L-methionineCombined sources1 Publication1
Active sitei79PROSITE-ProRule annotation1
Binding sitei376S-adenosyl-L-methionineCombined sources1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionMethyltransferase, RNA-binding, Transferase
Biological processtRNA processing
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc: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

EuPathDBiHostDB:ENSG00000107614.21
HGNCiHGNC:2977 TRDMT1
MIMi602478 gene
neXtProtiNX_O14717

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi1787
OpenTargetsiENSG00000107614
PharmGKBiPA162406922

Chemistry databases

DrugBankiDB04077 Glycerol
DB00738 Pentamidine
DB01752 S-Adenosyl-L-Homocysteine

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

EPDiO14717
PaxDbiO14717
PeptideAtlasiO14717
PRIDEiO14717
ProteomicsDBi48175
48176 [O14717-2]
48177 [O14717-3]
48178 [O14717-4]
48179 [O14717-5]
48180 [O14717-6]

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 Expressed in 158 organ(s), highest expression level in caput epididymis
CleanExiHS_TRDMT1
ExpressionAtlasiO14717 baseline and differential
GenevisibleiO14717 HS

Organism-specific databases

HPAiCAB009468
HPA036945
HPA036946

Interactioni

Protein-protein interaction databases

BioGridi108124, 14 interactors
IntActiO14717, 15 interactors
STRINGi9606.ENSP00000367030

Structurei

Secondary structure

1391
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni13 – 15S-adenosyl-L-methionine bindingCombined sources1 Publication3
Regioni57 – 58S-adenosyl-L-methionine bindingCombined sources1 Publication2

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0919 Eukaryota
COG0270 LUCA
GeneTreeiENSGT00390000016416
HOVERGENiHBG051385
InParanoidiO14717
KOiK15336
OMAiRLMSFPE
OrthoDBiEOG091G0FXV
PhylomeDBiO14717
TreeFamiTF300024

Family and domain databases

InterProiView protein in InterPro
IPR001525 C5_MeTfrase
IPR031303 C5_meth_CS
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF00145 DNA_methylase, 1 hit
PRINTSiPR00105 C5METTRFRASE
SUPFAMiSSF53335 SSF53335, 1 hit
TIGRFAMsiTIGR00675 dcm, 1 hit
PROSITEiView protein in PROSITE
PS00095 C5_MTASE_2, 1 hit
PS51679 SAM_MT_C5, 1 hit

Sequences (6+)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket
Note: Additional isoforms seem to exist.

This entry has 6 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q7Z3E4Q7Z3E4_HUMAN
tRNA (cytosine(38)-C(5))-methyltran...
TRDMT1 DKFZp686N1286
69Annotation score:
B7Z8H2B7Z8H2_HUMAN
cDNA FLJ52038, highly similar to DN...
TRDMT1
254Annotation score:
H0Y2T8H0Y2T8_HUMAN
tRNA (cytosine(38)-C(5))-methyltran...
TRDMT1
227Annotation score:
A0A0B4J214A0A0B4J214_HUMAN
tRNA (cytosine(38)-C(5))-methyltran...
TRDMT1
136Annotation score:
A0A0C4DG18A0A0C4DG18_HUMAN
tRNA (cytosine(38)-C(5))-methyltran...
TRDMT1
53Annotation score:
H0Y4A2H0Y4A2_HUMAN
tRNA (cytosine(38)-C(5))-methyltran...
TRDMT1
86Annotation score:

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 → Y1 PublicationCorresponds to variant dbSNP:rs11254413Ensembl.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
AC067747 Genomic DNA No translation available.
AL133415 Genomic DNA No translation available.
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
Hs.733857

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

Similar proteinsi

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
AC067747 Genomic DNA No translation available.
AL133415 Genomic DNA No translation available.
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
Hs.733857

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, 15 interactors
STRINGi9606.ENSP00000367030

Chemistry databases

DrugBankiDB04077 Glycerol
DB00738 Pentamidine
DB01752 S-Adenosyl-L-Homocysteine

PTM databases

iPTMnetiO14717
PhosphoSitePlusiO14717

Polymorphism and mutation databases

BioMutaiTRDMT1

Proteomic databases

EPDiO14717
PaxDbiO14717
PeptideAtlasiO14717
PRIDEiO14717
ProteomicsDBi48175
48176 [O14717-2]
48177 [O14717-3]
48178 [O14717-4]
48179 [O14717-5]
48180 [O14717-6]

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
EuPathDBiHostDB:ENSG00000107614.21
GeneCardsiTRDMT1
HGNCiHGNC:2977 TRDMT1
HPAiCAB009468
HPA036945
HPA036946
MIMi602478 gene
neXtProtiNX_O14717
OpenTargetsiENSG00000107614
PharmGKBiPA162406922
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0919 Eukaryota
COG0270 LUCA
GeneTreeiENSGT00390000016416
HOVERGENiHBG051385
InParanoidiO14717
KOiK15336
OMAiRLMSFPE
OrthoDBiEOG091G0FXV
PhylomeDBiO14717
TreeFamiTF300024

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiTRDMT1 human
EvolutionaryTraceiO14717
GeneWikiiTRDMT1
GenomeRNAii1787
PROiPR:O14717
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000107614 Expressed in 158 organ(s), highest expression level in caput epididymis
CleanExiHS_TRDMT1
ExpressionAtlasiO14717 baseline and differential
GenevisibleiO14717 HS

Family and domain databases

InterProiView protein in InterPro
IPR001525 C5_MeTfrase
IPR031303 C5_meth_CS
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF00145 DNA_methylase, 1 hit
PRINTSiPR00105 C5METTRFRASE
SUPFAMiSSF53335 SSF53335, 1 hit
TIGRFAMsiTIGR00675 dcm, 1 hit
PROSITEiView protein in PROSITE
PS00095 C5_MTASE_2, 1 hit
PS51679 SAM_MT_C5, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTRDMT_HUMAN
AccessioniPrimary (citable) accession number: O14717
Secondary accession number(s): B0YJ02
, B0YJ03, B0YJ07, B0YJ08, O43669, Q86WW6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: January 1, 1998
Last modified: November 7, 2018
This is version 160 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
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