6PZV | pdb_00006pzv

Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	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	ubiquitin_1	e6pzvA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	ubiquitin_1	e6pzvB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
E	ubiquitin_1	e6pzvE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	ubiquitin_1	e6pzvF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	DNMT1-RFD	e6pzvC2	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)
C	DNMT1-RFD_C	e6pzvC1	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)
G	DNMT1-RFD	e6pzvG1	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)
G	DNMT1-RFD_C	e6pzvG2	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	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
C	1.10.10.2230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)
G	1.10.10.2230	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	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
C, G	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E, F	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organismal-level homeostasis homeostatic process energy homeostasis regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development forebrain neuron differentiation sexual reproduction organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cell cycle cell cycle process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination regulation of proteolysis involved in protein catabolic process regulation of proteolysis proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process male meiosis I male meiotic nuclear division male gamete generation connective tissue development adipose tissue development fat pad development tissue development female gonad development female sex differentiation development of primary female sexual characteristics establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body
C, G	DNA (cytosine-5)-methyltransferase 1	DNA binding binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates DNA binding binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding chromatin binding promoter-specific chromatin binding	regulation of cellular process negative regulation of biological process 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 heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular process negative regulation of biological process 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 heterochromatin formation 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 constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of gene expression via chromosomal CpG island methylation methylation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
D, H	Histone H3.3	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process cellular developmental process ossification cell differentiation osteoblast differentiation cell population proliferation negative regulation of biological process chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process pericentric heterochromatin formation regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation 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 macromolecule metabolic process regulation of metabolic process sexual reproduction fertilization single fertilization regulation of centromere complex assembly protein-containing complex organization chromosome organization protein-DNA complex assembly regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization cellular component biogenesis protein-DNA complex organization organelle organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly centromere complex assembly multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation female gamete generation gamete generation oocyte development anatomical structure maturation germ cell development oocyte maturation oocyte differentiation cell maturation nucleosome assembly nucleosome organization spermatid development spermatid differentiation spermatogenesis male gamete generation negative regulation of cellular component organization regulation of chromosome condensation negative regulation of chromosome condensation negative regulation of chromosome organization negative regulation of organelle organization chromosome condensation subtelomeric heterochromatin formation telomere organization muscle structure development muscle cell differentiation nucleus organization multicellular organism growth developmental growth	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle membraneless organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome protein-DNA complex nucleosome chromatin sex chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen Barr body nuclear lumen X chromosome nucleoplasm chromosome, telomeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR019954	Ubiquitin conserved site	Conserved Site
A, B, E, F	IPR050158	Ubiquitin and ubiquitin-like	Family
A, B, E, F	IPR000626	Ubiquitin-like domain	Domain
A, B, E, F	IPR019956	Ubiquitin domain	Domain
A, B, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, G	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
C, G	IPR017198	DNA (cytosine-5)-methyltransferase 1-like	Family
C, G	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C, G	IPR010506	DMAP1-binding domain	Domain
C, G	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
C, G	IPR050390	DNA Cytosine-5 Methyltransferase	Family
C, G	IPR001025	Bromo adjacent homology (BAH) domain	Domain
C, G	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
C, G	IPR002857	Zinc finger, CXXC-type	Domain
C, G	IPR001525	C-5 cytosine methyltransferase	Family
C, G	IPR022702	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Domain
D, H	IPR000164	Histone H3/CENP-A	Family
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR007125	Histone H2A/H2B/H3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E, F	Pharos: P0CG47	astrocytic tumor cleft soft palate lung cancer Cleft of hard palate ovarian cancer isolated cleft palate
D, H	Pharos: P84243	malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial intellectual disability lung cancer malignant mesothelioma pituitary cancer atopic eczema subependymal giant cell astrocytoma breast cancer cutaneous lupus erythematosus glioma susceptibility 1 invasive ductal breast carcinoma malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma plasma cell myeloma atypical teratoid rhabdoid tumor subependymoma breast carcinoma Down syndrome exocrine pancreatic carcinoma hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D, H	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.