3SWC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   GLP (G9A-LIKE PROTEIN) SET DOMAIN IN COMPLEX WITH DNMT3AK44ME2 PEPTIDE

Authors :   Y. Chang, J. R. Horton, X. Zhang, X. Cheng

Date :   13 Jul 11 (Deposition) - 30 Nov 11 (Release) - 30 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

Chains :   Asym. Unit : A,B,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)
Biol. Unit 3: A,B,P,Q  (1x)

Keywords :   Epigenetics, Non-Histone Lysine Methylation, Set Domain, Protein Lysine Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Chang, L. Sun, K. Kokura, J. R. Horton, M. Fukuda, A. Espejo, V. Izumi J. M. Koomen, M. T. Bedford, X. Zhang, Y. Shinkai, J. Fang, X. Cheng
Mpp8 Mediates The Interactions Between Dna Methyltransferas Dnmt3A And H3K9 Methyltransferase Glp/G9A.
Nat Commun V. 2 533 2011
PubMed-ID: 22086334 | Reference-DOI: 10.1038/NCOMMS1549

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE EHMT1
	Chains	:	A, B
	EC Number	:	2.1.1.-, 2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PXC681
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 982-1266
	Gene	:	EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 1, EU- HMTASE1, G9A-LIKE PROTEIN 1, GLP, GLP1, HISTONE H3-K9 METHYLTRANSFERASE 5, H3-K9-HMTASE 5, LYSINE N-METHYLTRANSFERASE 1D

Molecule 2 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A
	Chains	:	P, Q
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 39-50
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	DNMT3A, DNA METHYLTRANSFERASE MMUIIIA, DNA MTASE MMUIIIA, M.MMUIIIA
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		B		Q
Biological Unit 3 (1x)	:	A	B	P	Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	MLY	2	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	MLY	2	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:1031 , CYS A:1044 , CYS A:1074 , CYS A:1078	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	CYS A:1037 , CYS A:1074 , CYS A:1080 , CYS A:1084	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	CYS A:1031 , CYS A:1033 , CYS A:1037 , CYS A:1042	BINDING SITE FOR RESIDUE ZN A 303
04	AC4	SOFTWARE	CYS A:1172 , CYS A:1225 , CYS A:1227 , CYS A:1232	BINDING SITE FOR RESIDUE ZN A 304
05	AC5	SOFTWARE	MET A:1105 , TRP A:1107 , SER A:1141 , TYR A:1142 , ARG A:1166 , ASN A:1169 , HIS A:1170 , TYR A:1211 , PHE A:1223 , SER A:1224 , CYS A:1225 , ARG A:1226 , ARG P:47	BINDING SITE FOR RESIDUE SAH A 202
06	AC6	SOFTWARE	CYS B:1031 , CYS B:1044 , CYS B:1074 , CYS B:1078	BINDING SITE FOR RESIDUE ZN B 305
07	AC7	SOFTWARE	ZN B:307 , CYS B:1037 , CYS B:1074 , CYS B:1080 , CYS B:1084	BINDING SITE FOR RESIDUE ZN B 306
08	AC8	SOFTWARE	ZN B:306 , CYS B:1031 , CYS B:1033 , CYS B:1037 , CYS B:1042	BINDING SITE FOR RESIDUE ZN B 307
09	AC9	SOFTWARE	CYS B:1172 , CYS B:1225 , CYS B:1227 , CYS B:1232	BINDING SITE FOR RESIDUE ZN B 308
10	BC1	SOFTWARE	MET B:1105 , GLY B:1106 , TRP B:1107 , SER B:1141 , TYR B:1142 , ARG B:1166 , PHE B:1167 , ASN B:1169 , HIS B:1170 , TYR B:1211 , PHE B:1215 , PHE B:1223 , CYS B:1225 , ARG B:1226 , ARG Q:47	BINDING SITE FOR RESIDUE SAH B 201

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

Asymmetric Unit

No.	Residues
1	Arg P:47	-	Pro P:48

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069183	C	1075	Y	EHMT1_HUMAN	Disease (KLESTS)	---	A/B	C	1044	Y
2	UniProt	VAR_036346	Y	1173	F	EHMT1_HUMAN	Unclassified	---	A/B	Y	1142	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069183	C	1075	Y	EHMT1_HUMAN	Disease (KLESTS)	---	A	C	1044	Y
2	UniProt	VAR_036346	Y	1173	F	EHMT1_HUMAN	Unclassified	---	A	Y	1142	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069183	C	1075	Y	EHMT1_HUMAN	Disease (KLESTS)	---	B	C	1044	Y
2	UniProt	VAR_036346	Y	1173	F	EHMT1_HUMAN	Unclassified	---	B	Y	1142	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069183	C	1075	Y	EHMT1_HUMAN	Disease (KLESTS)	---	A/B	C	1044	Y
2	UniProt	VAR_036346	Y	1173	F	EHMT1_HUMAN	Unclassified	---	A/B	Y	1142	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	EHMT1_HUMAN	1060-1123	2	A:1029-1092 B:1029-1092
2	SET	PS50280	SET domain profile.	EHMT1_HUMAN	1126-1243	2	A:1095-1212 B:1095-1212

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	EHMT1_HUMAN	1060-1123	1	A:1029-1092 -
2	SET	PS50280	SET domain profile.	EHMT1_HUMAN	1126-1243	1	A:1095-1212 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	EHMT1_HUMAN	1060-1123	1	- B:1029-1092
2	SET	PS50280	SET domain profile.	EHMT1_HUMAN	1126-1243	1	- B:1095-1212

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRE_SET	PS50867	Pre-SET domain profile.	EHMT1_HUMAN	1060-1123	2	A:1029-1092 B:1029-1092
2	SET	PS50280	SET domain profile.	EHMT1_HUMAN	1126-1243	2	A:1095-1212 B:1095-1212

(no "Exon" information available for 3SWC)

Asymmetric 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:261
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:261
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265 
         EHMT1_HUMAN   1006 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee............ee..............hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhhh......eeeee.....eeeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------PRE_SET  PDB: A:1029-1092 UniProt: 1060-1123                    --SET  PDB: A:1095-1212 UniProt: 1126-1243                                                                              ----------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3swc A  975 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1235
                                   984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:261
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265 
         EHMT1_HUMAN   1006 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............eee...........ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeee..eeeehhhhhhh......eee.........eeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------PRE_SET  PDB: B:1029-1092 UniProt: 1060-1123                    --SET  PDB: B:1095-1212 UniProt: 1126-1243                                                                              ----------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3swc B  975 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1235
                                   984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with DNM3A_MOUSE | O88508 from UniProtKB/Swiss-Prot  Length:908

    Alignment length:9
         DNM3A_MOUSE     41 TARKVGRPG   49
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                3swc P   41 TARkVGRPG   49
                               |     
                               |     
                              44-MLY

Chain Q from PDB  Type:PROTEIN  Length:8
 aligned with DNM3A_MOUSE | O88508 from UniProtKB/Swiss-Prot  Length:908

    Alignment length:8
         DNM3A_MOUSE     42 ARKVGRPG   49
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                3swc Q   42 ARkVGRPG   49
                              |     
                             44-MLY

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 3SWC)

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

(no "Pfam Domain" information available for 3SWC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (EHMT1_HUMAN | Q9H9B1)

molecular function
	GO:0070742	C2H2 zinc finger domain binding	Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
	GO:0046976	histone methyltransferase activity (H3-K27 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 of the histone H3 protein.
	GO:0046974	histone methyltransferase activity (H3-K9 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein.
	GO:0018024	histone-lysine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	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:0016279	protein-lysine N-methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0009790	embryo development	The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
	GO:0070734	histone H3-K27 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone.
	GO:0051567	histone H3-K9 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
	GO:0034968	histone lysine methylation	The modification of a histone by addition of one or more methyl groups to a lysine residue.
	GO:0016571	histone methylation	The modification of histones by addition of methyl groups.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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:0018027	peptidyl-lysine dimethylation	The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
	GO:0018026	peptidyl-lysine monomethylation	The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0060992	response to fungicide	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 fungicide stimulus. Fungicides are chemicals used to kill fungi.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	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.

Chain P,Q (DNM3A_MOUSE | O88508)

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:0051719	DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates	Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing CpN = S-adenosyl-L-homocysteine + DNA containing 5-MeCpN.
	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: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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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: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.
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: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:0043045	DNA methylation involved in embryo development	The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression.
	GO:0043046	DNA methylation involved in gamete generation	The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete.
	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: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: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: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:0071361	cellular response to ethanol	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 ethanol stimulus.
	GO:0071456	cellular response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0097284	hepatocyte apoptotic process	Any apoptotic process in a hepatocyte, the main structural component of the liver.
	GO:0044027	hypermethylation of CpG island	An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes.
	GO:0010216	maintenance of DNA methylation	Any process involved in maintaining the methylation state of a nucleotide sequence.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006346	methylation-dependent chromatin silencing	Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	GO:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	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:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0010942	positive regulation of cell death	Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	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:0006349	regulation of gene expression by genetic imprinting	Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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:0042220	response to cocaine	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 cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
	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: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: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: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:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0001741	XY body	A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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.

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3svm
3sw9	GLP SET DOMAIN IN COMPLEX WITH DNMT3AK44ME0 PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File