3PTA | pdb_00003pta

Crystal structure of human DNMT1(646-1600) in complex with DNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ptaa3	All beta proteins	SH3-like barrel	BAH domain	BAH domain	BAH domains from DNA methyltransferase 1 (DNMT1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ptaa5	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)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ptaa1	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)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ptaa2	Peptides	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain-like	DNMT1 CXXC-BAH1 linker domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CXXC zinc-finger domain	8053031	3002156	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053033	3001462	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8053034	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BAH domain	8053032	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)
A	BAH_1	e3ptaA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_1	ECOD (1.6)
A	BAH_2	e3ptaA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BAH_2	ECOD (1.6)
A	DNA_methylase	e3ptaA1	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	e3ptaA4	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	e3ptaA5	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
C	DNA (5'-D(CPCPTPGPCPGPGPAPGPGPCPTPCPAPCPGPGPGP*A)-3')	-	-	-
A	DNA (cytosine-5)-methyltransferase 1	RNA binding binding lncRNA binding nucleic acid binding DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates RNA binding binding lncRNA binding nucleic acid binding DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates chromatin binding promoter-specific chromatin binding DNA binding DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates sequence-specific DNA binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule 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 macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process methylation 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 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 heterochromatin formation constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation 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 chromosomal DNA methylation maintenance following DNA replication 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 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 RNA biosynthetic 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen pericentric heterochromatin intracellular membraneless organelle chromatin chromosome heterochromatin chromosomal region membraneless organelle chromosome, centromeric region replication fork germ cell nucleus female germ cell nucleus
B	DNA (5'-D(TPCPCPCPGPTPGPAPGPCPCPTPCPCPGPCPAPGP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001025	Bromo adjacent homology (BAH) domain	Domain
A	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A	IPR002857	Zinc finger, CXXC-type	Domain
A	IPR022702	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Domain
A	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
A	IPR017198	DNA (cytosine-5)-methyltransferase 1-like	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR010506	DMAP1-binding domain	Domain
A	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
A	IPR050390	DNA Cytosine-5 Methyltransferase	Family
A	IPR001525	C-5 cytosine methyltransferase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P26358	hereditary sensory neuropathy-deafness-dementia syndrome medulloblastoma tubular adenocarcinoma carcinoma melanotic medulloblastoma hearing loss disorder prostate cancer hereditary sensory and autonomic neuropathy type 4 sarcomatoid carcinoma breast carcinoma Charcot-Marie-Tooth disease malignant colon neoplasm Clear-cell metastatic renal cell carcinoma adenocarcinoma prostate intraepithelial neoplasia hereditary sensory neuropathy-deafness-dementia syndrome medulloblastoma tubular adenocarcinoma carcinoma melanotic medulloblastoma hearing loss disorder prostate cancer hereditary sensory and autonomic neuropathy type 4 sarcomatoid carcinoma breast carcinoma Charcot-Marie-Tooth disease malignant colon neoplasm Clear-cell metastatic renal cell carcinoma adenocarcinoma prostate intraepithelial neoplasia childhood medulloblastoma dementia medullomyoblastoma with myogenic differentiation adult medulloblastoma granular cell carcinoma peripheral neuropathy asthma autosomal dominant cerebellar ataxia, deafness and narcolepsy breast cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma chronic myelomonocytic leukemia acute myeloid leukemia cribriform carcinoma dermatomyositis gastric cancer myopathy pancreatic intraductal papillary-mucinous neoplasm hereditary sensory and autonomic neuropathy psoriasis astrocytic tumor benign colon neoplasm ulcerative colitis juvenile dermatomyositis cribriform carcinoma of breast adrenal cortex carcinoma desmoplastic/nodular medulloblastoma anxiety disorder gastric neoplasm hematologic disease peripheral nervous system disease hereditary sensory and autonomic neuropathy type 1 rheumatoid arthritis hereditary sensory and autonomic neuropathy type 5 schizophrenia bipolar disorder sensory peripheral neuropathy cancer intellectual disability undifferentiated carcinoma Kleine-Levin syndrome malignant mesothelioma colonic neoplasm myelodysplastic syndrome ovarian cancer hereditary diffuse gastric adenocarcinoma hereditary sensory and autonomic neuropathy type 2 Riley-Day syndrome

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.