4DA4 | pdb_00004da4

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	MatP	e4da4B2	A: a/b three-layered sandwiches	X: C-terminal domain in some PLP-dependent transferases	H: C-terminal domain in some PLP-dependent transferases	T: C-terminal domain in some PLP-dependent transferases	F: MatP	ECOD (v294.1)
B	Cobalamin_bind	e4da4B4	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
A	Death	e4da4A4	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: Death	ECOD (v294.1)
A	MatP	e4da4A1	A: a/b three-layered sandwiches	X: C-terminal domain in some PLP-dependent transferases	H: C-terminal domain in some PLP-dependent transferases	T: C-terminal domain in some PLP-dependent transferases	F: MatP	ECOD (v294.1)

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	RNA binding binding lncRNA binding nucleic acid binding histone deacetylase binding protein binding enzyme binding chromatin binding promoter-specific chromatin binding DNA binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity RNA binding binding lncRNA binding nucleic acid binding histone deacetylase binding protein binding enzyme binding chromatin binding promoter-specific chromatin binding DNA 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 histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K18ub reader activity molecular adaptor activity DNA (cytosine-5-)-methyltransferase activity DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates S-adenosylmethionine-dependent methyltransferase activity histone H3K14ub reader activity histone H3K23ub reader 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 biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process response to stimulus response to chemical response to xenobiotic stimulus regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process methylation cellular response to bisphenol A cellular response to stimulus cellular response to chemical stimulus response to oxygen-containing compound cellular response to oxygen-containing compound response to bisphenol A cellular component organization chromatin organization cellular component organization or biogenesis chromosomal DNA methylation maintenance following DNA replication cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process negative regulation of gene expression via chromosomal CpG island methylation chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic 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 cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive 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 macrophage fusion positive regulation of cellular component organization regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion regulation of developmental process cell-cell fusion positive regulation of developmental process anatomical structure development syncytium formation developmental process positive regulation of macrophage fusion positive regulation of syncytium formation by plasma membrane fusion syncytium formation by plasma membrane fusion anatomical structure morphogenesis regulation of macrophage fusion anatomical structure formation involved in morphogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex 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	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
A, B	IPR050390	DNA Cytosine-5 Methyltransferase	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.