CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005497
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA (cytosine-5)-methyltransferase 1 
Protein Synonyms/Alias
 Dnmt1; CXXC-type zinc finger protein 9; DNA methyltransferase HsaI; DNA MTase HsaI; M.HsaI; MCMT 
Gene Name
 DNMT1 
Gene Synonyms/Alias
 AIM; CXXC9; DNMT 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
58EFLQTEIKNQLCDLEubiquitination[1]
70DLETKLRKEELSEEGubiquitination[1]
83EGYLAKVKSLLNKDLubiquitination[1]
88KVKSLLNKDLSLENGubiquitination[1]
401PQMLTNEKLSIFDANubiquitination[2]
602PCMRDLIKLAGVTLGubiquitination[1, 2, 3]
682CQQPECGKCKACKDMubiquitination[1]
691KACKDMVKFGGSGRSubiquitination[1, 3]
755SWVGEAVKTDGKKSYubiquitination[1]
897ARFESPPKTQPTEDNubiquitination[1]
905TQPTEDNKFKFCVSCubiquitination[1]
944VLYYSATKNGILYRVubiquitination[1]
977SPVKRPRKEPVDEDLubiquitination[1]
991LYPEHYRKYSDYIKGubiquitination[1]
997RKYSDYIKGSNLDAPubiquitination[1, 2]
1013PYRIGRIKEIFCPKKubiquitination[1, 3]
1036DIKIRVNKFYRPENTubiquitination[1]
1108FLEAYNAKSKSFEDPubiquitination[1]
1110EAYNAKSKSFEDPPNubiquitination[1]
1151SEPEIEIKLPKLRTLubiquitination[1]
1230RGQRLPQKGDVEMLCubiquitination[1]
1339LAAAPGEKLPLFPEPubiquitination[1]
1365SVVVDDKKFVSNITRubiquitination[1]
1431ILRDHICKDMSALVAubiquitination[1]
1499CSCVEAGKACDPAARubiquitination[1]
1551TNPEPMGKQGRVLHPubiquitination[2]
1588LFGNILDKHRQVGNAubiquitination[1]
1602AVPPPLAKAIGLEIKubiquitination[1]
Reference
 [1] 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]
 [2] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [3] 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] 
Functional Description
 Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. 
Sequence Annotation
 DOMAIN 755 880 BAH 1.
 DOMAIN 972 1100 BAH 2.
 REPEAT 1109 1110 1.
 REPEAT 1111 1112 2.
 REPEAT 1113 1114 3.
 REPEAT 1115 1116 4.
 REPEAT 1117 1118 5.
 REPEAT 1119 1120 6; approximate.
 ZN_FING 646 692 CXXC-type.
 REGION 1 336 Interaction with the PRC2/EED-EZH2
 REGION 1 148 Interaction with DNMT3A.
 REGION 1 120 Interaction with DMAP1.
 REGION 149 217 Interaction with DNMT3B.
 REGION 163 174 Interaction with PCNA.
 REGION 308 606 Interaction with the PRC2/EED-EZH2
 REGION 310 502 Homodimerization.
 REGION 331 550 DNA replication foci-targeting sequence
 REGION 651 697 Required for activity.
 REGION 693 754 Autoinhibitory linker.
 REGION 1109 1120 6 X 2 AA tandem repeats of K-G.
 REGION 1121 1616 Interaction with the PRC2/EED-EZH2
 REGION 1139 1616 Catalytic.
 MOTIF 177 205 Nuclear localization signal (Potential).
 ACT_SITE 1226 1226
 METAL 353 353 Zinc.
 METAL 356 356 Zinc.
 METAL 414 414 Zinc.
 METAL 418 418 Zinc.
 MOD_RES 70 70 N6,N6-dimethyllysine.
 MOD_RES 127 127 Phosphoserine.
 MOD_RES 133 133 Phosphoserine.
 MOD_RES 142 142 N6-methyllysine; by SETD7.
 MOD_RES 143 143 Phosphoserine; by PKB/AKT1.
 MOD_RES 152 152 Phosphoserine.
 MOD_RES 154 154 Phosphoserine.
 MOD_RES 160 160 N6-acetyllysine.
 MOD_RES 173 173 N6-acetyllysine.
 MOD_RES 188 188 N6-acetyllysine.
 MOD_RES 259 259 N6-acetyllysine.
 MOD_RES 288 288 Phosphoserine (By similarity).
 MOD_RES 366 366 N6-acetyllysine.
 MOD_RES 394 394 Phosphoserine.
 MOD_RES 509 509 Phosphoserine (By similarity).
 MOD_RES 714 714 Phosphoserine.
 MOD_RES 732 732 Phosphoserine.
 MOD_RES 749 749 N6-acetyllysine.
 MOD_RES 891 891 N6-acetyllysine.
 MOD_RES 957 957 N6-acetyllysine.
 MOD_RES 961 961 N6-acetyllysine.
 MOD_RES 975 975 N6-acetyllysine.
 MOD_RES 1054 1054 N6-acetyllysine.
 MOD_RES 1111 1111 N6-acetyllysine.
 MOD_RES 1113 1113 N6-acetyllysine.
 MOD_RES 1115 1115 N6-acetyllysine.
 MOD_RES 1117 1117 N6-acetyllysine; by EHMT2.
 MOD_RES 1349 1349 N6-acetyllysine.
 MOD_RES 1415 1415 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Activator; Alternative splicing; Chromatin regulator; Complete proteome; Disease mutation; DNA-binding; Metal-binding; Methylation; Methyltransferase; Neuropathy; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Repressor; S-adenosyl-L-methionine; Transcription; Transcription regulation; Transferase; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1616 AA 
Protein Sequence
MPARTAPARV PTLAVPAISL PDDVRRRLKD LERDSLTEKE CVKEKLNLLH EFLQTEIKNQ 60
LCDLETKLRK EELSEEGYLA KVKSLLNKDL SLENGAHAYN REVNGRLENG NQARSEARRV 120
GMADANSPPK PLSKPRTPRR SKSDGEAKRS RDPPASASQV TGIRAEPSPS PRITRKSTRQ 180
TTITSHFAKG PAKRKPQEES ERAKSDESIK EEDKDQDEKR RRVTSRERVA RPLPAEEPER 240
AKSGTRTEKE EERDEKEEKR LRSQTKEPTP KQKLKEEPDR EARAGVQADE DEDGDEKDEK 300
KHRSQPKDLA AKRRPEEKEP EKVNPQISDE KDEDEKEEKR RKTTPKEPTE KKMARAKTVM 360
NSKTHPPKCI QCGQYLDDPD LKYGQHPPDA VDEPQMLTNE KLSIFDANES GFESYEALPQ 420
HKLTCFSVYC KHGHLCPIDT GLIEKNIELF FSGSAKPIYD DDPSLEGGVN GKNLGPINEW 480
WITGFDGGEK ALIGFSTSFA EYILMDPSPE YAPIFGLMQE KIYISKIVVE FLQSNSDSTY 540
EDLINKIETT VPPSGLNLNR FTEDSLLRHA QFVVEQVESY DEAGDSDEQP IFLTPCMRDL 600
IKLAGVTLGQ RRAQARRQTI RHSTREKDRG PTKATTTKLV YQIFDTFFAE QIEKDDREDK 660
ENAFKRRRCG VCEVCQQPEC GKCKACKDMV KFGGSGRSKQ ACQERRCPNM AMKEADDDEE 720
VDDNIPEMPS PKKMHQGKKK KQNKNRISWV GEAVKTDGKK SYYKKVCIDA ETLEVGDCVS 780
VIPDDSSKPL YLARVTALWE DSSNGQMFHA HWFCAGTDTV LGATSDPLEL FLVDECEDMQ 840
LSYIHSKVKV IYKAPSENWA MEGGMDPESL LEGDDGKTYF YQLWYDQDYA RFESPPKTQP 900
TEDNKFKFCV SCARLAEMRQ KEIPRVLEQL EDLDSRVLYY SATKNGILYR VGDGVYLPPE 960
AFTFNIKLSS PVKRPRKEPV DEDLYPEHYR KYSDYIKGSN LDAPEPYRIG RIKEIFCPKK 1020
SNGRPNETDI KIRVNKFYRP ENTHKSTPAS YHADINLLYW SDEEAVVDFK AVQGRCTVEY 1080
GEDLPECVQV YSMGGPNRFY FLEAYNAKSK SFEDPPNHAR SPGNKGKGKG KGKGKPKSQA 1140
CEPSEPEIEI KLPKLRTLDV FSGCGGLSEG FHQAGISDTL WAIEMWDPAA QAFRLNNPGS 1200
TVFTEDCNIL LKLVMAGETT NSRGQRLPQK GDVEMLCGGP PCQGFSGMNR FNSRTYSKFK 1260
NSLVVSFLSY CDYYRPRFFL LENVRNFVSF KRSMVLKLTL RCLVRMGYQC TFGVLQAGQY 1320
GVAQTRRRAI ILAAAPGEKL PLFPEPLHVF APRACQLSVV VDDKKFVSNI TRLSSGPFRT 1380
ITVRDTMSDL PEVRNGASAL EISYNGEPQS WFQRQLRGAQ YQPILRDHIC KDMSALVAAR 1440
MRHIPLAPGS DWRDLPNIEV RLSDGTMARK LRYTHHDRKN GRSSSGALRG VCSCVEAGKA 1500
CDPAARQFNT LIPWCLPHTG NRHNHWAGLY GRLEWDGFFS TTVTNPEPMG KQGRVLHPEQ 1560
HRVVSVRECA RSQGFPDTYR LFGNILDKHR QVGNAVPPPL AKAIGLEIKL CMLAKARESA 1620
SAKIKEEEAA KD 1632 
Gene Ontology
 GO:0005721; C:centromeric heterochromatin; IEA:Compara.
 GO:0005634; C:nucleus; TAS:ProtInc.
 GO:0005657; C:replication fork; IEA:Compara.
 GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IDA:UniProtKB.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 GO:0008327; F:methyl-CpG binding; IEA:Compara.
 GO:0003723; F:RNA binding; IEA:Compara.
 GO:0008270; F:zinc ion binding; IEA:Compara.
 GO:0071230; P:cellular response to amino acid stimulus; IEA:Compara.
 GO:0016568; P:chromatin modification; IEA:UniProtKB-KW.
 GO:0016458; P:gene silencing; IEA:Compara.
 GO:0010216; P:maintenance of DNA methylation; IDA:UniProtKB.
 GO:0051573; P:negative regulation of histone H3-K9 methylation; IMP:UniProtKB.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; TAS:ProtInc.
 GO:0010628; P:positive regulation of gene expression; IMP:UniProtKB.
 GO:0051571; P:positive regulation of histone H3-K4 methylation; IMP:UniProtKB.
 GO:0042127; P:regulation of cell proliferation; IEA:Compara.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR001025; BAH_dom.
 IPR018117; C5_DNA_meth_AS.
 IPR001525; C5_MeTfrase.
 IPR022702; Cytosine_MeTrfase1_RFD.
 IPR010506; DMAP1-bd.
 IPR017198; DNA_C5-MeTrfase_1_euk.
 IPR002857; Znf_CXXC. 
Pfam
 PF01426; BAH
 PF06464; DMAP_binding
 PF00145; DNA_methylase
 PF12047; DNMT1-RFD
 PF02008; zf-CXXC 
SMART
 SM00439; BAH 
PROSITE
 PS51038; BAH
 PS00094; C5_MTASE_1
 PS00095; C5_MTASE_2
 PS51058; ZF_CXXC 
PRINTS
 PR00105; C5METTRFRASE.