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Q9UJW3 (DNM3L_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA (cytosine-5)-methyltransferase 3-like
Gene names
Name:DNMT3L
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length386 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalytically inactive regulatory factor of DNA methyltransferases. It is essential for the function of DNMT3A and DNMT3B. Activates DNMT3A and DNMT3B by binding to their catalytic domain. Accelerates the binding of DNA and AdoMet to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases. Recognizes unmethylated histone H3 lysine 4 (H3K4) and induces de novo DNA methylation by recruitment or activation of DNMT3. Ref.5

Subunit structure

Homodimer. Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with histone H3 (via N-terminus). Ref.5 Ref.6

Subcellular location

Nucleus Probable.

Tissue specificity

Expressed at low levels in several tissues including testis, ovary, and thymus.

Miscellaneous

Interaction with histone H3 is strongly inhibited by methylation at lysine 4 (H3K4me).

Sequence similarities

Contains 1 ADD domain.

Contains 1 GATA-type zinc finger.

Contains 1 PHD-type zinc finger.

Ontologies

Keywords
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA methylation

Non-traceable author statement PubMed 12202768. Source: UniProtKB

chorionic trophoblast cell differentiation

Inferred from electronic annotation. Source: Ensembl

in utero embryonic development

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription, DNA-templated

Inferred from direct assay PubMed 12202768. Source: UniProtKB

placenta development

Inferred from electronic annotation. Source: Ensembl

regulation of gene expression by genetic imprinting

Non-traceable author statement PubMed 12202768. Source: UniProtKB

spermatogenesis

Non-traceable author statement PubMed 11934864. Source: UniProtKB

   Cellular_componentcondensed nuclear chromosome

Inferred from electronic annotation. Source: Ensembl

cytosol

Inferred from direct assay PubMed 16780588. Source: UniProtKB

nuclear heterochromatin

Inferred from electronic annotation. Source: Ensembl

nucleus

Inferred from direct assay PubMed 16780588. Source: UniProtKB

   Molecular_functionenzyme activator activity

Inferred from direct assay PubMed 16543361. Source: MGI

enzyme binding

Inferred from physical interaction PubMed 12202768. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction Ref.6. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

HDAC1Q135473EBI-740967,EBI-301834

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Note: Other splice isoforms seem to exist.
Isoform 1 (identifier: Q9UJW3-1)

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.
Isoform 2 (identifier: Q9UJW3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     332-332: S → SS

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 386386DNA (cytosine-5)-methyltransferase 3-like
PRO_0000088047

Regions

Domain41 – 173133ADD
Zinc finger52 – 8231GATA-type; atypical
Zinc finger93 – 14957PHD-type; atypical

Natural variations

Alternative sequence3321S → SS in isoform 2.
VSP_041295
Natural variant2781R → G. Ref.4
Corresponds to variant rs7354779 [ dbSNP | Ensembl ].
VAR_051962

Experimental info

Mutagenesis2611F → A: Loss of binding to DNMT3A. Ref.6
Sequence conflict2461P → A in AAF05812. Ref.1
Sequence conflict2661L → F in AAF05812. Ref.1

Secondary structure

............................................................ 386
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 31, 2011. Version 3.
Checksum: 65EC2AB7492D53B3

FASTA38643,583
        10         20         30         40         50         60 
MAAIPALDPE AEPSMDVILV GSSELSSSVS PGTGRDLIAY EVKANQRNIE DICICCGSLQ 

        70         80         90        100        110        120 
VHTQHPLFEG GICAPCKDKF LDALFLYDDD GYQSYCSICC SGETLLICGN PDCTRCYCFE 

       130        140        150        160        170        180 
CVDSLVGPGT SGKVHAMSNW VCYLCLPSSR SGLLQRRRKW RSQLKAFYDR ESENPLEMFE 

       190        200        210        220        230        240 
TVPVWRRQPV RVLSLFEDIK KELTSLGFLE SGSDPGQLKH VVDVTDTVRK DVEEWGPFDL 

       250        260        270        280        290        300 
VYGATPPLGH TCDRPPSWYL FQFHRLLQYA RPKPGSPRPF FWMFVDNLVL NKEDLDVASR 

       310        320        330        340        350        360 
FLEMEPVTIP DVHGGSLQNA VRVWSNIPAI RSRHWALVSE EELSLLAQNK QSSKLAAKWP 

       370        380 
TKLVKNCFLP LREYFKYFST ELTSSL 

« Hide

Isoform 2 [UniParc].

Checksum: 699AAC1929D473A9
Show »

FASTA38743,670

References

« Hide 'large scale' references
[1]"Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family."
Aapola U., Shibuya K., Scott H.S., Ollila J., Vihinen M., Heino M., Shintani A., Kawasaki K., Minoshima S., Krohn K., Antonarakis S.E., Shimizu N., Kudoh J., Peterson P.
Genomics 65:293-298(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ALTERNATIVE SPLICING.
[2]"The DNA sequence of human chromosome 21."
Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A. expand/collapse author list , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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 1), VARIANT GLY-278.
Tissue: Placenta.
[5]"DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA."
Ooi S.K., Qiu C., Bernstein E., Li K., Jia D., Yang Z., Erdjument-Bromage H., Tempst P., Lin S.-P., Allis C.D., Cheng X., Bestor T.H.
Nature 448:714-717(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), FUNCTION, HOMODIMERIZATION.
[6]"Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation."
Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., Cheng X.
Nature 449:248-251(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS) OF 160-387, SUBUNIT, MUTAGENESIS OF PHE-261.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF194032 mRNA. Translation: AAF05812.1.
AP001753 Genomic DNA. Translation: BAA95556.1.
AP001059 Genomic DNA. No translation available.
AP001060 Genomic DNA. No translation available.
CH471079 Genomic DNA. Translation: EAX09445.1.
BC002560 mRNA. Translation: AAH02560.1.
CCDSCCDS13705.1. [Q9UJW3-2]
CCDS46650.1. [Q9UJW3-1]
RefSeqNP_037501.2. NM_013369.3. [Q9UJW3-2]
NP_787063.1. NM_175867.2. [Q9UJW3-1]
UniGeneHs.592165.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2PV0X-ray3.30A/B/C1-386[»]
2PVCX-ray3.69A/B/C1-386[»]
2QRVX-ray2.89B/C/F/G160-386[»]
ProteinModelPortalQ9UJW3.
SMRQ9UJW3. Positions 34-380.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid118984. 11 interactions.
DIPDIP-35238N.
IntActQ9UJW3. 7 interactions.
MINTMINT-1448248.
STRING9606.ENSP00000270172.

Protein family/group databases

REBASE4636. M.HsaDnmt3L.

PTM databases

PhosphoSiteQ9UJW3.

Polymorphism databases

DMDM334302913.

Proteomic databases

PaxDbQ9UJW3.
PRIDEQ9UJW3.

Protocols and materials databases

DNASU29947.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000270172; ENSP00000270172; ENSG00000142182. [Q9UJW3-2]
ENST00000418993; ENSP00000412862; ENSG00000142182. [Q9UJW3-1]
GeneID29947.
KEGGhsa:29947.
UCSCuc002zeg.2. human. [Q9UJW3-1]
uc002zeh.2. human. [Q9UJW3-2]

Organism-specific databases

CTD29947.
GeneCardsGC21M045666.
HGNCHGNC:2980. DNMT3L.
MIM606588. gene.
neXtProtNX_Q9UJW3.
PharmGKBPA27447.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG69419.
HOGENOMHOG000246422.
HOVERGENHBG051382.
InParanoidQ9UJW3.
KOK17400.
OMATVPVWKR.
TreeFamTF329039.

Gene expression databases

ArrayExpressQ9UJW3.
BgeeQ9UJW3.
CleanExHS_DNMT3L.
GenevestigatorQ9UJW3.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR025766. ADD.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51533. ADD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9UJW3.
GeneWikiDNMT3L.
GenomeRNAi29947.
NextBio52621.
PROQ9UJW3.
SOURCESearch...

Entry information

Entry nameDNM3L_HUMAN
AccessionPrimary (citable) accession number: Q9UJW3
Secondary accession number(s): E9PB42, Q9BUJ4
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: May 31, 2011
Last modified: July 9, 2014
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 21

Human chromosome 21: entries, gene names and cross-references to MIM