3PT6 | pdb_00003pt6

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d3pt6b3	All beta proteins	SH3-like barrel	BAH domain	BAH domain	BAH domains from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d3pt6b5	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C5 cytosine-specific DNA methylase, DCM	Methyltransferase domain from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d3pt6b1	Small proteins	bi-CXXC zinc finger-like	bi-CXXC zinc finger-like	bi-CXXC zinc finger-like	Zn finger domain from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d3pt6b2	Peptides	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3pt6a3	All beta proteins	SH3-like barrel	BAH domain	BAH domain	BAH domains from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3pt6a5	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C5 cytosine-specific DNA methylase, DCM	Methyltransferase domain from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3pt6a1	Small proteins	bi-CXXC zinc finger-like	bi-CXXC zinc finger-like	bi-CXXC zinc finger-like	Zn finger domain from DNA methyltransferase 1 (DNMT1)	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3pt6a2	Peptides	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2 Family	CXXC zinc-finger domain	8049704	4006601	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Family	BAH domain	8053021	4002595	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Family	BAH domain	8053022	4002595	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Family	C5 cytosine-specific DNA methylase, DCM	8053023	4003611	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Superfamily	CXXC zinc-finger domain	8053024	3002156	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Superfamily	BAH domain	8053026	3001462	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Superfamily	BAH domain	8053027	3001462	SCOP2 (2022-06-29)
F [auth B]	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053025	3000118	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053027	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053026	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXXC zinc-finger domain	8053024	3002156	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053025	3000118	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)
F [auth B]	BAH_1	e3pt6B2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_1	ECOD (1.6)
F [auth B]	BAH_2	e3pt6B3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_2	ECOD (1.6)
F [auth B]	DNA_methylase	e3pt6B1	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)
F [auth B]	zf-CXXC	e3pt6B4	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)
F [auth B]	EUF08665	e3pt6B5	A: few secondary structure elements	X: CXXC domain-like	H: C-terminal Zn-binding domain in DNA (cytosine-5)-methyltransferase 1 (From Topology)	T: C-terminal Zn-binding domain in DNA (cytosine-5)-methyltransferase 1	F: EUF08665	ECOD (1.6)
A	BAH_1	e3pt6A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_1	ECOD (1.6)
A	BAH_2	e3pt6A3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_2	ECOD (1.6)
A	DNA_methylase	e3pt6A1	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	zf-CXXC	e3pt6A4	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)
A	EUF08665	e3pt6A5	A: few secondary structure elements	X: CXXC domain-like	H: C-terminal Zn-binding domain in DNA (cytosine-5)-methyltransferase 1 (From Topology)	T: C-terminal Zn-binding domain in DNA (cytosine-5)-methyltransferase 1	F: EUF08665	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth 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, F [auth B]	PF02008	CXXC zinc finger domain (zf-CXXC)	CXXC zinc finger domain	This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [ ...	This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].	Domain
A, F [auth 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, F [auth B]	DNA (cytosine-5)-methyltransferase 1	RNA binding binding lncRNA binding nucleic acid 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 RNA binding binding lncRNA binding nucleic acid 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 DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	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 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 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 nucleic acid biosynthetic process cellular response to bisphenol A cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical 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 regulation of primary metabolic process negative regulation of RNA 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 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 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 heterochromatin formation 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	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin membrane-bounded organelle nucleus germ cell nucleus 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 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
B [auth C], D	DNA (5'-D(TPCPCPCPGPTPGPAPGPCPCPTPCPCPGPCPAPGP*G)-3')	-	-	-
C [auth I], E [auth J]	DNA (5'-D(CPCPTPGPCPGPGPAPGPGPCPTPCPAPCPGPGPGP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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