5WVO | pdb_00005wvo

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d5wvob_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5wvoa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	e5wvoD01	A: Rossmann-like	X: Rossmann-related	H: FAD/NAD(P)-binding domain	T: Phage_lysozyme	F:	ECOD (20:10:01)
C	e5wvoC1	A: Cryptochrome/photolyase FAD-binding domain-related	X: Cryptochrome/photolyase FAD-binding domain-related	H: Undecaprenyl diphosphate synthase	T: RuBisCO_large_N	F:	ECOD (20:10:01)
B	e5wvoB1	A: P-loop domains-like	X: Cas7-related	H: CRISPR-associated protein Cas7f/Csy3	T: p450	F:	ECOD (20:10:01)
A	e5wvoA1	A: Cryptochrome/photolyase FAD-binding domain-related	X: Cryptochrome/photolyase FAD-binding domain-related	H: Undecaprenyl diphosphate synthase	T: RuBisCO_large_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF12047	Cytosine specific DNA methyltransferase replication foci domain (DNMT1-RFD)	Cytosine specific DNA methyltransferase replication foci domain	This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDA ...	This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties. [1]	Domain
A, B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Histone H3.1	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C	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 histone reader activity histone H3 reader activity chromatin-protein adaptor activity 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 histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K18ub reader activity molecular adaptor activity chromatin binding promoter-specific chromatin binding DNA binding histone H3K14ub reader activity DNA (cytosine-5-)-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K23ub reader 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 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 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 component biogenesis cellular component assembly heterochromatin formation heterochromatin organization 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
A, B	Ubiquitin	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane nucleoplasm organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle cytosolic ribosome ribosome protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex synapse cell junction endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cytosolic small ribosomal subunit small ribosomal subunit ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR009072	Histone-fold	Homologous Superfamily
D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D	IPR000164	Histone H3/CENP-A	Family
C	IPR001025	Bromo adjacent homology (BAH) domain	Domain
C	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
C	IPR002857	Zinc finger, CXXC-type	Domain
C	IPR022702	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Domain
C	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C	IPR010506	DMAP1-binding domain	Domain
C	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
C	IPR050390	DNA Cytosine-5 Methyltransferase	Family
C	IPR001525	C-5 cytosine methyltransferase	Family
A, B	IPR019954	Ubiquitin conserved site	Conserved Site
A, B	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
A, B	IPR050158	Ubiquitin and ubiquitin-like	Family
A, B	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
A, B	IPR000626	Ubiquitin-like domain	Domain
A, B	IPR002906	Small ribosomal subunit protein eS31	Domain
A, B	IPR019956	Ubiquitin domain	Domain
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
C	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 peripheral nervous system disease hematologic 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
A, B	Pharos: P62979	acute myeloid leukemia large cell medulloblastoma Diamond-Blackfan anemia lung carcinoma hematopoietic and lymphoid system neoplasm ulcerative colitis