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O14717

- TRDMT_HUMAN

UniProt

O14717 - TRDMT_HUMAN

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Protein

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

Gene

TRDMT1

Organism
Homo sapiens (Human)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei79 – 791PROSITE-ProRule annotation

GO - Molecular functioni

  1. DNA (cytosine-5-)-methyltransferase activity Source: ProtInc
  2. DNA binding Source: InterPro
  3. RNA binding Source: UniProtKB-KW
  4. tRNA methyltransferase activity Source: MGI

GO - Biological processi

  1. C-5 methylation of cytosine Source: GOC
  2. response to amphetamine Source: Ensembl
  3. tRNA methylation Source: MGI
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.

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
ProteomesiUP000005640: Chromosome 10

Organism-specific databases

HGNCiHGNC:2977. TRDMT1.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. cytoplasm Source: MGI
  2. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162406922.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 391391tRNA (cytosine(38)-C(5))-methyltransferasePRO_0000088040Add
BLAST

Proteomic databases

MaxQBiO14717.
PaxDbiO14717.
PRIDEiO14717.

PTM databases

PhosphoSiteiO14717.

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

BgeeiO14717.
CleanExiHS_TRDMT1.
ExpressionAtlasiO14717. baseline and differential.
GenevestigatoriO14717.

Organism-specific databases

HPAiCAB009468.
HPA036946.

Interactioni

Protein-protein interaction databases

BioGridi108124. 14 interactions.
IntActiO14717. 13 interactions.
STRINGi9606.ENSP00000367030.

Structurei

Secondary structure

1
391
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Helixi15 – 239Combined sources
Beta strandi26 – 338Combined sources
Helixi37 – 4610Combined sources
Helixi57 – 593Combined sources
Helixi62 – 687Combined sources
Beta strandi71 – 755Combined sources
Helixi98 – 1058Combined sources
Helixi106 – 1083Combined sources
Beta strandi114 – 1218Combined sources
Helixi124 – 1263Combined sources
Helixi128 – 13912Combined sources
Beta strandi142 – 1498Combined sources
Helixi151 – 1544Combined sources
Beta strandi162 – 17211Combined sources
Beta strandi182 – 1854Combined sources
Helixi253 – 2564Combined sources
Helixi263 – 2664Combined sources
Helixi270 – 2767Combined sources
Helixi277 – 2793Combined sources
Turni295 – 2995Combined sources
Beta strandi307 – 3093Combined sources
Helixi316 – 3216Combined sources
Turni322 – 3254Combined sources
Helixi328 – 3369Combined sources
Helixi345 – 3517Combined sources
Helixi366 – 37510Combined sources
Helixi379 – 39012Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G55X-ray1.80A2-391[»]
ProteinModelPortaliO14717.
SMRiO14717. Positions 2-189, 248-391.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO14717.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 391388SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd
BLAST

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

eggNOGiCOG0270.
GeneTreeiENSGT00390000016416.
HOVERGENiHBG051385.
InParanoidiO14717.
KOiK15336.
OMAiFGVPYSR.
PhylomeDBiO14717.
TreeFamiTF300024.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR025813. DNA/tRNA_C5-MeTrfase.
IPR029063. SAM-dependent_MTases-like.
[Graphical view]
PANTHERiPTHR10629. PTHR10629. 1 hit.
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. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti148 – 1481L → I in AAC39764. (PubMed:9592134)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti101 – 1011H → Y.1 Publication
Corresponds to variant rs11254413 [ dbSNP | Ensembl ].
VAR_051961

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei59 – 10749GITLE…LDILP → RPLDTNNRKLWLSVPRVYII SNLSWHSKFKATIFSYCKAS VRAITLSSP in isoform F. 1 PublicationVSP_005634Add
BLAST
Alternative sequencei59 – 7113GITLE…RLSFD → ITKITKVYSFGKC in isoform E. 1 PublicationVSP_005632Add
BLAST
Alternative sequencei59 – 635GITLE → DWPAG in isoform D. 1 PublicationVSP_005630
Alternative sequencei64 – 391328Missing in isoform D. 1 PublicationVSP_005631Add
BLAST
Alternative sequencei72 – 391320Missing in isoform E. 1 PublicationVSP_005633Add
BLAST
Alternative sequencei84 – 12946Missing in isoform C. 1 PublicationVSP_005629Add
BLAST
Alternative sequencei84 – 10724Missing in isoform B. 1 PublicationVSP_005628Add
BLAST
Alternative sequencei108 – 391284Missing in isoform F. 1 PublicationVSP_005635Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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_004403.1. NM_004412.5. [O14717-1]
XP_005252432.1. XM_005252375.2. [O14717-3]
UniGeneiHs.351665.

Genome annotation databases

EnsembliENST00000377799; ENSP00000367030; ENSG00000107614. [O14717-1]
ENST00000424636; ENSP00000389497; ENSG00000107614.
ENST00000495022; ENSP00000417594; ENSG00000107614. [O14717-4]
ENST00000525762; ENSP00000431476; ENSG00000107614.
GeneIDi1787.
KEGGihsa:1787.
UCSCiuc001iop.3. human. [O14717-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS7114.1. [O14717-1 ]
RefSeqi NP_004403.1. NM_004412.5. [O14717-1 ]
XP_005252432.1. XM_005252375.2. [O14717-3 ]
UniGenei Hs.351665.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1G55 X-ray 1.80 A 2-391 [» ]
ProteinModelPortali O14717.
SMRi O14717. Positions 2-189, 248-391.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 108124. 14 interactions.
IntActi O14717. 13 interactions.
STRINGi 9606.ENSP00000367030.

Chemistry

DrugBanki DB00738. Pentamidine.

PTM databases

PhosphoSitei O14717.

Proteomic databases

MaxQBi O14717.
PaxDbi O14717.
PRIDEi O14717.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000377799 ; ENSP00000367030 ; ENSG00000107614 . [O14717-1 ]
ENST00000424636 ; ENSP00000389497 ; ENSG00000107614 .
ENST00000495022 ; ENSP00000417594 ; ENSG00000107614 . [O14717-4 ]
ENST00000525762 ; ENSP00000431476 ; ENSG00000107614 .
GeneIDi 1787.
KEGGi hsa:1787.
UCSCi uc001iop.3. human. [O14717-1 ]

Organism-specific databases

CTDi 1787.
GeneCardsi GC10M017098.
HGNCi HGNC:2977. TRDMT1.
HPAi CAB009468.
HPA036946.
MIMi 602478. gene.
neXtProti NX_O14717.
PharmGKBi PA162406922.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0270.
GeneTreei ENSGT00390000016416.
HOVERGENi HBG051385.
InParanoidi O14717.
KOi K15336.
OMAi FGVPYSR.
PhylomeDBi O14717.
TreeFami TF300024.

Enzyme and pathway databases

BioCyci MetaCyc:HS03011-MONOMER.

Miscellaneous databases

ChiTaRSi TRDMT1. human.
EvolutionaryTracei O14717.
GeneWikii TRDMT1.
GenomeRNAii 1787.
NextBioi 7271.
PROi O14717.
SOURCEi Search...

Gene expression databases

Bgeei O14717.
CleanExi HS_TRDMT1.
ExpressionAtlasi O14717. baseline and differential.
Genevestigatori O14717.

Family and domain databases

Gene3Di 3.40.50.150. 1 hit.
InterProi IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR025813. DNA/tRNA_C5-MeTrfase.
IPR029063. SAM-dependent_MTases-like.
[Graphical view ]
PANTHERi PTHR10629. PTHR10629. 1 hit.
Pfami PF00145. DNA_methylase. 1 hit.
[Graphical view ]
PRINTSi PR00105. C5METTRFRASE.
SUPFAMi SSF53335. SSF53335. 2 hits.
TIGRFAMsi TIGR00675. dcm. 1 hit.
PROSITEi PS00095. C5_MTASE_2. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast."
    Yoder J.A., Bestor T.H.
    Hum. Mol. Genet. 7:279-284(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
  2. "Cloning and analysis of a novel human putative DNA methyltransferase."
    Van den Wyngaert I., Sprengel J., Kass S.U., Luyten W.H.M.L.
    FEBS Lett. 426:283-289(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
  3. "Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells."
    Okano M., Xie S., Li E.
    Nucleic Acids Res. 26:2536-2540(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A).
    Tissue: Heart.
  4. NHLBI resequencing and genotyping service (RS&G)
    Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  5. "The DNA sequence and comparative analysis of human chromosome 10."
    Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J.
    , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
    Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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] (ISOFORM A), VARIANT TYR-101.
    Tissue: Uterus.
  8. "Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes."
    Franchina M., Hooper J., Kay P.H.
    Int. J. Biochem. Cell Biol. 33:1104-1115(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 19-179 (ISOFORMS A; B; C; D; E AND F).
    Tissue: Peripheral blood leukocyte.
  9. Cited for: FUNCTION, CATALYTIC ACTIVITY.
  10. "Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA."
    Dong A., Yoder J.A., Zhang X., Zhou L., Bestor T.H., Cheng X.
    Nucleic Acids Res. 29:439-448(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

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: October 29, 2014
This is version 125 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

External Data

Dasty 3