4DA4

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	BAH domain	8053027	3001462	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053025	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	BAH domain	8053026	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053027	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053025	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053026	3001462	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	BAH_1	e4da4B3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_1	ECOD (1.6)
B	BAH_2	e4da4B4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_2	ECOD (1.6)
B	DNA_methylase	e4da4B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase	ECOD (1.6)
A	BAH_1	e4da4A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_1	ECOD (1.6)
A	BAH_2	e4da4A4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_2	ECOD (1.6)
A	DNA_methylase	e4da4A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.30.490	Mainly Beta	Roll	SH3 type barrels.	Bromo adjacent homology (BAH) domain	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.90.120.10	Alpha Beta	Alpha-Beta Complex	DNA Methylase	Chain A, domain 2	CATH (4.3.0)
A	2.30.30.490	Mainly Beta	Roll	SH3 type barrels.	Bromo adjacent homology (BAH) domain	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.90.120.10	Alpha Beta	Alpha-Beta Complex	DNA Methylase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01426	BAH domain (BAH)	BAH domain	This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction [3].	Domain
A, B	PF00145	C-5 cytosine-specific DNA methylase (DNA_methylase)	C-5 cytosine-specific DNA methylase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA (cytosine-5)-methyltransferase 1	histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA binding organic cyclic compound binding nucleic acid binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA binding organic cyclic compound binding nucleic acid binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding protein domain specific binding DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid RNA binding DNA (cytosine-5-)-methyltransferase activity DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates S-adenosylmethionine-dependent methyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process S-adenosylmethionine metabolic process sulfur compound metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic cyclic compound biosynthetic process cellular response to bisphenol A cellular response to stimulus response to organic substance cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to organic substance response to organic cyclic compound response to bisphenol A cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of RNA biosynthetic process cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor regulation of vascular associated smooth muscle cell proliferation cell population proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation negative regulation of phenotypic switching multicellular organismal process smooth muscle cell differentiation cellular developmental process regulation of developmental process regulation of smooth muscle cell differentiation regulation of cell differentiation negative regulation of muscle cell differentiation muscle cell differentiation muscle structure development regulation of cell differentiation involved in phenotypic switching multicellular organism development vascular associated smooth muscle cell differentiation cell differentiation involved in phenotypic switching regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching cell differentiation anatomical structure development negative regulation of cell differentiation system development developmental process negative regulation of developmental process vascular associated smooth muscle cell differentiation involved in phenotypic switching reversible differentiation negative regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching phenotypic switching vasculature development circulatory system development negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation regulation of phenotypic switching negative regulation of cell differentiation involved in phenotypic switching DNA methylation-dependent heterochromatin formation heterochromatin formation facultative heterochromatin formation epigenetic programming of gene expression muscle cell apoptotic process smooth muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death regulation of smooth muscle cell apoptotic process negative regulation of vascular associated smooth muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of apoptotic process negative regulation of muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process apoptotic process programmed cell death	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex protein-DNA complex chromatin chromosome heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex protein-DNA complex chromatin chromosome heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus germ cell nucleus intracellular membrane-bounded organelle female germ cell nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin chromosomal region chromosome, centromeric region replication fork
C, E	DNA_UPPER_STRAND	-	-	-
D, F	DNA_LOWER_STRAND	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001025	Bromo adjacent homology (BAH) domain	Domain
A, B	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, B	IPR022702	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Domain
A, B	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
A, B	IPR017198	DNA (cytosine-5)-methyltransferase 1-like	Family
A, B	IPR010506	DMAP1-binding domain	Domain
A, B	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
A, B	IPR001525	C-5 cytosine methyltransferase	Family
A, B	IPR002857	Zinc finger, CXXC-type	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.