3EPZ

Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNMT1-RFD	e3epzA1	A: beta barrels	X: Replication foci-targeting sequence N-terminal domain (From Topology)	H: Replication foci-targeting sequence N-terminal domain (From Topology)	T: Replication foci-targeting sequence N-terminal domain	F: DNMT1-RFD	ECOD (1.6)
A	DNMT1-RFD_C	e3epzA2	A: alpha arrays	X: HTH	H: Replication foci-targeting sequence C-terminal domain (From Topology)	T: Replication foci-targeting sequence C-terminal domain	F: DNMT1-RFD_C	ECOD (1.6)
B	DNMT1-RFD	e3epzB1	A: beta barrels	X: Replication foci-targeting sequence N-terminal domain (From Topology)	H: Replication foci-targeting sequence N-terminal domain (From Topology)	T: Replication foci-targeting sequence N-terminal domain	F: DNMT1-RFD	ECOD (1.6)
B	DNMT1-RFD_C	e3epzB2	A: alpha arrays	X: HTH	H: Replication foci-targeting sequence C-terminal domain (From Topology)	T: Replication foci-targeting sequence C-terminal domain	F: DNMT1-RFD_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.2230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	1.10.10.2230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA (cytosine-5)-methyltransferase 1	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 RNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin 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 RNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA binding DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity 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 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 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 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic cyclic compound biosynthetic process DNA methylation-dependent heterochromatin formation heterochromatin formation facultative heterochromatin formation epigenetic programming of gene expression cellular response to bisphenol A cellular response to stimulus response to organic substance response to stimulus cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to organic substance response to organic cyclic compound response to bisphenol A 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 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex pericentric heterochromatin membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex pericentric heterochromatin protein-DNA complex chromatin chromosome heterochromatin chromosomal region intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle replication fork germ cell nucleus female germ cell nucleus

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	IPR002857	Zinc finger, CXXC-type	Domain
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	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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 cribriform carcinoma acute myeloid leukemia dermatomyositis gastric cancer myopathy pancreatic intraductal papillary-mucinous neoplasm hereditary sensory and autonomic neuropathy psoriasis astrocytic tumor benign colon neoplasm juvenile dermatomyositis ulcerative colitis cribriform carcinoma of breast desmoplastic/nodular medulloblastoma adrenal cortex carcinoma gastric neoplasm anxiety disorder hematologic disease peripheral nervous system disease hereditary sensory and autonomic neuropathy type 1 hereditary sensory and autonomic neuropathy type 5 rheumatoid arthritis schizophrenia bipolar disorder intellectual disability sensory peripheral neuropathy cancer Kleine-Levin syndrome undifferentiated carcinoma 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 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.