3PT9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE DNMT1(731-1602) IN THE FREE STATE

Authors :   J. Song, D. J. Patel

Date :   02 Dec 10 (Deposition) - 29 Dec 10 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Maintenance Dna Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Song, O. Rechkoblit, T. H. Bestor, D. J. Patel
Structure Of Dnmt1-Dna Complex Reveals A Role For Autoinhibition In Maintenance Dna Methylation.
Science V. 331 1036 2011
PubMed-ID: 21163962 | Reference-DOI: 10.1126/SCIENCE.1195380

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 1
	Chains	:	A
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21-RIL(DE3)
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 731-1602
	Gene	:	DNMT1, DNMT, MET1, UIM
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	DNMT1, MET-1, DNA METHYLTRANSFERASE MMUI, DNA MTASE MMUI, M.MMUI, MCMT

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3 , HOH A:7 , HOH A:39 , HOH A:193 , HOH A:315 , PHE A:1148 , SER A:1149 , GLY A:1150 , GLY A:1152 , GLY A:1153 , LEU A:1154 , GLU A:1171 , MET A:1172 , TRP A:1173 , GLU A:1192 , ASP A:1193 , CYS A:1194 , GLY A:1226 , PRO A:1228 , LEU A:1250 , PRO A:1489 , ALA A:1581 , VAL A:1582	BINDING SITE FOR RESIDUE SAH A 1603
2	AC2	SOFTWARE	CYS A:1479 , CYS A:1481 , CYS A:1487 , HIS A:1504	BINDING SITE FOR RESIDUE ZN A 1
3	AC3	SOFTWARE	HIS A:796 , CYS A:823 , CYS A:897 , CYS A:900	BINDING SITE FOR RESIDUE ZN A 2

(no "SS Bond" information available for 3PT9)

(no "Cis Peptide Bond" information available for 3PT9)

(no "SAP(SNP)/Variant" information available for 3PT9)

Asymmetric/Biological Unit (4, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	DNMT1_MOUSE	758-884 976-1103	2	A:758-884 A:976-1103
2	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	DNMT1_MOUSE	1142-1601	1	A:1142-1600
3	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	DNMT1_MOUSE	1221-1233	1	A:1221-1233
4	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	DNMT1_MOUSE	1576-1594	1	A:1576-1594

Asymmetric/Biological Unit (16, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSMUST00000004202	1	ENSMUSE00000502170	chr9:20757317-20757152	166	DNMT1_MOUSE	1-27	27	0	-	-
1.2	ENSMUST00000004202	2	ENSMUSE00000217265	chr9:20747063-20747027	37	DNMT1_MOUSE	27-39	13	0	-	-
1.3	ENSMUST00000004202	3	ENSMUSE00000217269	chr9:20746250-20746143	108	DNMT1_MOUSE	40-75	36	0	-	-
1.4	ENSMUST00000004202	4	ENSMUSE00000217268	chr9:20746027-20745817	211	DNMT1_MOUSE	76-146	71	0	-	-
1.5	ENSMUST00000004202	5	ENSMUSE00000440704	chr9:20744998-20744920	79	DNMT1_MOUSE	146-172	27	0	-	-
1.6	ENSMUST00000004202	6	ENSMUSE00000217242	chr9:20742590-20742515	76	DNMT1_MOUSE	172-197	26	0	-	-
1.7	ENSMUST00000004202	7	ENSMUSE00000217270	chr9:20741637-20741606	32	DNMT1_MOUSE	198-208	11	0	-	-
1.8	ENSMUST00000004202	8	ENSMUSE00000217249	chr9:20741065-20740987	79	DNMT1_MOUSE	208-234	27	0	-	-
1.9	ENSMUST00000004202	9	ENSMUSE00000217261	chr9:20739003-20738963	41	DNMT1_MOUSE	235-248	14	0	-	-
1.10	ENSMUST00000004202	10	ENSMUSE00000217246	chr9:20736643-20736559	85	DNMT1_MOUSE	248-276	29	0	-	-
1.11	ENSMUST00000004202	11	ENSMUSE00000489733	chr9:20734609-20734569	41	DNMT1_MOUSE	277-290	14	0	-	-
1.12	ENSMUST00000004202	12	ENSMUSE00000638437	chr9:20733573-20733492	82	DNMT1_MOUSE	290-317	28	0	-	-
1.13	ENSMUST00000004202	13	ENSMUSE00000217275	chr9:20731615-20731551	65	DNMT1_MOUSE	318-339	22	0	-	-
1.14	ENSMUST00000004202	14	ENSMUSE00000297925	chr9:20731292-20731250	43	DNMT1_MOUSE	339-353	15	0	-	-
1.15	ENSMUST00000004202	15	ENSMUSE00000297902	chr9:20731155-20731075	81	DNMT1_MOUSE	354-380	27	0	-	-
1.16	ENSMUST00000004202	16	ENSMUSE00000217247	chr9:20730998-20730889	110	DNMT1_MOUSE	381-417	37	0	-	-
1.17	ENSMUST00000004202	17	ENSMUSE00000217264	chr9:20728585-20728467	119	DNMT1_MOUSE	417-457	41	0	-	-
1.18	ENSMUST00000004202	18	ENSMUSE00000297849	chr9:20728238-20728146	93	DNMT1_MOUSE	457-488	32	0	-	-
1.19	ENSMUST00000004202	19	ENSMUSE00000217254	chr9:20727361-20727210	152	DNMT1_MOUSE	488-538	51	0	-	-
1.20	ENSMUST00000004202	20	ENSMUSE00000217278	chr9:20726925-20726738	188	DNMT1_MOUSE	539-601	63	0	-	-
1.21	ENSMUST00000004202	21	ENSMUSE00000217272	chr9:20726644-20726467	178	DNMT1_MOUSE	601-660	60	0	-	-
1.22	ENSMUST00000004202	22	ENSMUSE00000217271	chr9:20724650-20724553	98	DNMT1_MOUSE	661-693	33	0	-	-
1.23	ENSMUST00000004202	23	ENSMUSE00000217257	chr9:20724431-20724284	148	DNMT1_MOUSE	693-742	50	1	A:730-742	13
1.24	ENSMUST00000004202	24	ENSMUSE00000217252	chr9:20722994-20722879	116	DNMT1_MOUSE	743-781	39	1	A:743-781	39
1.25	ENSMUST00000004202	25	ENSMUSE00000217258	chr9:20722764-20722560	205	DNMT1_MOUSE	781-849	69	1	A:781-849	69
1.26	ENSMUST00000004202	26	ENSMUSE00000217241	chr9:20722486-20722350	137	DNMT1_MOUSE	850-895	46	1	A:850-895 (gaps)	46
1.27	ENSMUST00000004202	27	ENSMUSE00000217263	chr9:20721914-20721741	174	DNMT1_MOUSE	895-953	59	1	A:895-953	59
1.28	ENSMUST00000004202	28	ENSMUSE00000217280	chr9:20720384-20720166	219	DNMT1_MOUSE	953-1026	74	1	A:953-1026 (gaps)	74
1.29	ENSMUST00000004202	29	ENSMUSE00000217274	chr9:20718533-20718341	193	DNMT1_MOUSE	1026-1090	65	1	A:1026-1090	65
1.30	ENSMUST00000004202	30	ENSMUSE00000217277	chr9:20717100-20717016	85	DNMT1_MOUSE	1091-1119	29	1	A:1091-1110	20
1.31	ENSMUST00000004202	31	ENSMUSE00000217279	chr9:20716752-20716624	129	DNMT1_MOUSE	1119-1162	44	1	A:1137-1162	26
1.32	ENSMUST00000004202	32	ENSMUSE00000217255	chr9:20716459-20716177	283	DNMT1_MOUSE	1162-1256	95	1	A:1162-1256	95
1.33	ENSMUST00000004202	33	ENSMUSE00000217262	chr9:20716002-20715861	142	DNMT1_MOUSE	1256-1303	48	1	A:1256-1303	48
1.34	ENSMUST00000004202	34	ENSMUSE00000217251	chr9:20714750-20714584	167	DNMT1_MOUSE	1304-1359	56	1	A:1304-1359	56
1.35	ENSMUST00000004202	35	ENSMUSE00000516732	chr9:20714314-20714137	178	DNMT1_MOUSE	1359-1418	60	1	A:1359-1418	60
1.36	ENSMUST00000004202	36	ENSMUSE00000517723	chr9:20713729-20713534	196	DNMT1_MOUSE	1419-1484	66	1	A:1419-1484	66
1.37	ENSMUST00000004202	37	ENSMUSE00000297455	chr9:20713196-20712916	281	DNMT1_MOUSE	1484-1577	94	1	A:1484-1577	94
1.38	ENSMUST00000004202	38	ENSMUSE00000217243	chr9:20712405-20712315	91	DNMT1_MOUSE	1578-1608	31	1	A:1578-1600	23
1.39	ENSMUST00000004202	39	ENSMUSE00000538826	chr9:20712005-20711650	356	DNMT1_MOUSE	1608-1620	13	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:824
 aligned with DNMT1_MOUSE | P13864 from UniProtKB/Swiss-Prot  Length:1620

    Alignment length:871
                                   739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599 
         DNMT1_MOUSE    730 NKDRISWLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKVIYKAPSENWAMEGGTDPETTLPGAEDGKTYFFQLWYNQEYARFESPPKTQPTEDNKHKFCLSCIRLAELRQKEMPKVLEQIEEVDGRVYCSSITKNGVVYRLGDSVYLPPEAFTFNIKVASPVKRPKKDPVNETLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKNFEDPPNHARSPGNKGKGKGKGKGKGKHQVSEPKEPEAAIKLPKLRTLDVFSGCGGLSEGFHQAGISETLWAIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEIQNGASNSEIPYNGEPLSWFQRQLRGSHYQPILRDHICKDMSPLVAARMRHIPLFPGSDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNGYSSTGALRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILDRHRQVGNAVPPPLAKAIGLEIKLCLLS 1600
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------              ----------------------------------------------------------------------BAH-3pt9A02 A:935-1103                                                                                                                                                   -------                          -----DNA_methylase-3pt9A01 A:1142-1596                                                                                                                                                                                                                                                                                                                                                                                                                                      ---- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------              ----------------------------------------------------------------------BAH-3pt9A03 A:935-1103                                                                                                                                                   -------                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeee....ee...eeee.eeee..eeee...eeee.........eeeee..eeee....eeeeeeeeee.hhh.hhhhh...eeeeeeeeeeee.hhh.eee.eee.....hhhhh.--------------..eeeeeeee....eee...............hhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee..eeee...eeee.............................hhhhhh.-------.......eeeeeeeeeeeee..eeeeeeeeeeeee..hhhhh.............eeee...eeeee.hhh.eeeeeee.hhh..hhhhhhhhh..eeeeeee...........hhhhh...--------------------------.....eeeeee....hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh...eee..hhhhhhhhhhh..................eeee.............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh...hhhhhhhhhhhhhh..eeeeeeee.hhhh.....eeeeeeee................hhhhh...eee..eee...............hhhhhhh............eee......hhhhhhhhh.....eee.......hhhhhhhhhh.......hhhhh....ee.....ee.......................hhhhhh...............hhhhhhhhhhhhhh.....................................hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------BAH  PDB: A:758-884 UniProt: 758-884                                                                                           -------------------------------------------------------------------------------------------BAH  PDB: A:976-1103 UniProt: 976-1103                                                                                          --------------------------------------SAM_MT_C5  PDB: A:1142-1600 UniProt: 1142-1601                                                                                                                                                                                                                                                                                                                                                                                                                              PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_1   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         ------ PROSITE (2)
           Transcript 1 (1) Exon 1.23    Exon 1.24  PDB: A:743-781              --------------------------------------------------------------------Exon 1.26  PDB: A:850-895 (gaps)              ---------------------------------------------------------Exon 1.28  PDB: A:953-1026 (gaps) UniProt: 953-1026                       ----------------------------------------------------------------Exon 1.30  PDB: A:1091-1110  ------------------------------------------Exon 1.32  PDB: A:1162-1256 UniProt: 1162-1256                                                 -----------------------------------------------Exon 1.34  PDB: A:1304-1359 UniProt: 1304-1359          -----------------------------------------------------------Exon 1.36  PDB: A:1419-1484 UniProt: 1419-1484                    ---------------------------------------------------------------------------------------------Exon 1.38 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.25  PDB: A:781-849 UniProt: 781-849                           ---------------------------------------------Exon 1.27  PDB: A:895-953 UniProt: 895-953                 ------------------------------------------------------------------------Exon 1.29  PDB: A:1026-1090 UniProt: 1026-1090                   ----------------------------Exon 1.31  PDB: A:1137-1162 [INCOMPLETE]    ---------------------------------------------------------------------------------------------Exon 1.33  PDB: A:1256-1303 UniProt: 1256-1303  -------------------------------------------------------Exon 1.35  PDB: A:1359-1418 UniProt: 1359-1418              -----------------------------------------------------------------Exon 1.37  PDB: A:1484-1577 UniProt: 1484-1577                                                ----------------------- Transcript 1 (2)
                3pt9 A  730 SKDRISWLGQPMKIEENRTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKVIYKAPSENWAMEG--------------KTYFFQLWYNQEYARFESPPKTQPTEDNKHKFCLSCIRLAELRQKEMPKVLEQIEEVDGRVYCSSITKNGVVYRLGDSVYLPPEAFTFNIKVASPVKRPKKDPVNETLYPEHYRKYS-------LDAPEPYRIGRIKEIHCGKKKGKVNEADIKLRLYKFYRPENTHRSYNGSYHTDINMLYWSDEEAVVNFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKNFEDPPNHARSPG--------------------------IKLPKLRTLDVFSGCGGLSEGFHQAGISETLWAIEMWDPAAQAFRLNNPGTTVFTEDCNVLLKLVMAGEVTNSLGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSYRRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEIQNGASNSEIPYNGEPLSWFQRQLRGSHYQPILRDHICKDMSPLVAARMRHIPLFPGSDWRDLPNIQVRLGDGVIAHKLQYTFHDVKNGYSSTGALRGVCSCAEGKACDPESRQFSTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDSYRFFGNILDRHRQVGNAVPPPLAKAIGLEIKLCLLS 1600
                                   739       749       759       769       779       789       799       809       819       829       839       849|        -     | 869       879       889       899       909       919       929       939       949       959       969       979 |     989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109|        -         -      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599 
                                                                                                                                                  850            865                                                                                                                 981     989                                                                                                                     1110                       1137

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3PT9)

(no "CATH Domain" information available for 3PT9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: DNA_methylase (15)

Mus musculus (Mouse) (2)

DNA_methylase-3pt9A01

A:1142-1596

Clan: no clan defined [family: BAH] (7)

Family: BAH (7)

Mus musculus (Mouse) (2)

2a	BAH-3pt9A02	A:935-1103
2b	BAH-3pt9A03	A:935-1103

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DNMT1_MOUSE | P13864)

molecular function
	GO:0003886	DNA (cytosine-5-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
	GO:0051718	DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	Catalysis of the reaction: S-adenosyl-L-methionine + CpG (in DNA) = S-adenosyl-L-homocysteine + 5-MeCpG (in DNA).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0009008	DNA-methyltransferase activity	Catalysis of the transfer of a methyl group to a DNA molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen receptor.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008327	methyl-CpG binding	Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:1990841	promoter-specific chromatin binding	Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0045322	unmethylated CpG binding	Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0090116	C-5 methylation of cytosine	The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule.
	GO:0044026	DNA hypermethylation	An increase in the epigenetic methylation of cytosine and adenosine residues in DNA.
	GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0032776	DNA methylation on cytosine	The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
	GO:0010424	DNA methylation on cytosine within a CG sequence	The covalent transfer of a methyl group to C-5 or N-4 of a cytosine located within a CG sequence in a DNA molecule.
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0046498	S-adenosylhomocysteine metabolic process	The chemical reactions and pathways involving S-adenosylhomocysteine; the L-enantiomer is formed from S-adenosylmethionine and is a strong inhibitor of S-adenosylmethionine-mediated methylation reactions. It can be cleaved to form adenosine and homocysteine.
	GO:0046499	S-adenosylmethioninamine metabolic process	The chemical reactions and pathways involving S-adenosylmethioninamine, (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt.
	GO:0046500	S-adenosylmethionine metabolic process	The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0071230	cellular response to amino acid stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
	GO:0071284	cellular response to lead ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
	GO:1990090	cellular response to nerve growth factor stimulus	A process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nerve growth factor stimulus.
	GO:0036120	cellular response to platelet-derived growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet-derived growth factor stimulus.
	GO:0071560	cellular response to transforming growth factor beta stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0016458	gene silencing	Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
	GO:0010216	maintenance of DNA methylation	Any process involved in maintaining the methylation state of a nucleotide sequence.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0051573	negative regulation of histone H3-K9 methylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0090309	positive regulation of methylation-dependent chromatin silencing	Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0014823	response to activity	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
	GO:0036276	response to antidepressant	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antidepressant stimulus, a mood-stimulating drug.
	GO:0031000	response to caffeine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0010212	response to ionizing radiation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
	GO:0010288	response to lead ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
	GO:0033189	response to vitamin A	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005721	pericentric heterochromatin	Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

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	DNMT1_MOUSE \| P13864
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	2.1.1.37
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	DNMT1_MOUSE \| P13864	:	3av4 3av5 3av6 3pt6 4da4 5wy1

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