CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-024011
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA (cytosine-5)-methyltransferase 3A 
Protein Synonyms/Alias
 Dnmt3a; DNA methyltransferase HsaIIIA; DNA MTase HsaIIIA; M.HsaIIIA 
Gene Name
 DNMT3A 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
200GDPYYISKRKRDEWLubiquitination[1, 2, 3]
367NKQPMYRKAIYEVLQubiquitination[1, 2, 3, 4]
783NPVMIDAKEVSAAHRubiquitination[4, 5]
906RHLFAPLKEYFACV*ubiquitination[4]
Reference
 [1] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [2] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [4] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [5] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Can actively repress transcription through the recruitment of HDAC activity (By similarity). 
Sequence Annotation
 DOMAIN 292 350 PWWP.
 DOMAIN 482 614 ADD.
 ZN_FING 493 523 GATA-type; atypical.
 ZN_FING 534 590 PHD-type; atypical.
 REGION 199 403 Interaction with DNMT1 and DNMT3B.
 REGION 494 586 Interaction with the PRC2/EED-EZH2
 REGION 641 645 S-adenosyl-L-methionine binding
 REGION 686 688 S-adenosyl-L-methionine binding
 REGION 891 893 S-adenosyl-L-methionine binding
 ACT_SITE 710 710 By similarity.
 BINDING 664 664 S-adenosyl-L-methionine (Probable).
 MOD_RES 105 105 Phosphoserine.
 MOD_RES 243 243 Phosphoserine.
 MOD_RES 255 255 Phosphoserine.
 MOD_RES 261 261 Phosphothreonine.
 MOD_RES 267 267 Phosphoserine.  
Keyword
 3D-structure; Alternative promoter usage; Alternative splicing; Chromatin regulator; Complete proteome; Cytoplasm; DNA-binding; Metal-binding; Methyltransferase; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repressor; S-adenosyl-L-methionine; Transferase; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 912 AA 
Protein Sequence
MPAMPSSGPG DTSSSAAERE EDRKDGEEQE EPRGKEERQE PSTTARKVGR PGRKRKHPPV 60
ESGDTPKDPA VISKSPSMAQ DSGASELLPN GDLEKRSEPQ PEEGSPAGGQ KGGAPAEGEG 120
AAETLPEASR AVENGCCTPK EGRGAPAEAG KEQKETNIES MKMEGSRGRL RGGLGWESSL 180
RQRPMPRLTF QAGDPYYISK RKRDEWLARW KREAEKKAKV IAGMNAVEEN QGPGESQKVE 240
EASPPAVQQP TDPASPTVAT TPEPVGSDAG DKNATKAGDD EPEYEDGRGF GIGELVWGKL 300
RGFSWWPGRI VSWWMTGRSR AAEGTRWVMW FGDGKFSVVC VEKLMPLSSF CSAFHQATYN 360
KQPMYRKAIY EVLQVASSRA GKLFPVCHDS DESDTAKAVE VQNKPMIEWA LGGFQPSGPK 420
GLEPPEEEKN PYKEVYTDMW VEPEAAAYAP PPPAKKPRKS TAEKPKVKEI IDERTRERLV 480
YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC 540
CGGREVLMCG NNNCCRCFCV ECVDLLVGPG AAQAAIKEDP WNCYMCGHKG TYGLLRRRED 600
WPSRLQMFFA NNHDQEFDPP KVYPPVPAEK RKPIRVLSLF DGIATGLLVL KDLGIQVDRY 660
IASEVCEDSI TVGMVRHQGK IMYVGDVRSV TQKHIQEWGP FDLVIGGSPC NDLSIVNPAR 720
KGLYEGTGRL FFEFYRLLHD ARPKEGDDRP FFWLFENVVA MGVSDKRDIS RFLESNPVMI 780
DAKEVSAAHR ARYFWGNLPG MNRPLASTVN DKLELQECLE HGRIAKFSKV RTITTRSNSI 840
KQGKDQHFPV FMNEKEDILW CTEMERVFGF PVHYTDVSNM SRLARQRLLG RSWSVPVIRH 900
LFAPLKEYFA CV 912 
Gene Ontology
 GO:0000775; C:chromosome, centromeric region; IEA:Compara.
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0000791; C:euchromatin; IDA:UniProtKB.
 GO:0005720; C:nuclear heterochromatin; IEA:Compara.
 GO:0016363; C:nuclear matrix; IDA:UniProtKB.
 GO:0003682; F:chromatin binding; IEA:Compara.
 GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IDA:UniProtKB.
 GO:0051718; F:DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates; IEA:Compara.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0045322; F:unmethylated CpG binding; IEA:Compara.
 GO:0071230; P:cellular response to amino acid stimulus; IEA:Compara.
 GO:0043045; P:DNA methylation involved in embryo development; IEA:Compara.
 GO:0043046; P:DNA methylation involved in gamete generation; IEA:Compara.
 GO:0010424; P:DNA methylation on cytosine within a CG sequence; IEA:Compara.
 GO:0044027; P:hypermethylation of CpG island; IEA:Compara.
 GO:0006346; P:methylation-dependent chromatin silencing; IEA:Compara.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0006349; P:regulation of gene expression by genetic imprinting; TAS:UniProtKB.
 GO:0046498; P:S-adenosylhomocysteine metabolic process; IEA:Compara.
 GO:0046499; P:S-adenosylmethioninamine metabolic process; IEA:Compara.
 GO:0007283; P:spermatogenesis; IEA:Compara. 
Interpro
 IPR025766; ADD.
 IPR018117; C5_DNA_meth_AS.
 IPR001525; C5_MeTfrase.
 IPR025811; C5_MeTrfase_3.
 IPR000313; PWWP.
 IPR011011; Znf_FYVE_PHD. 
Pfam
 PF00145; DNA_methylase
 PF00855; PWWP 
SMART
 SM00293; PWWP 
PROSITE
 PS51533; ADD
 PS00094; C5_MTASE_1
 PS00095; C5_MTASE_2
 PS50812; PWWP 
PRINTS