9MP0 | pdb_00009mp0

The cryo-EM structure of the human DNA methyltransferases DNMT3A2 and DNMT3L dodecamer

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth P], J [auth Q]	PF21255	DNMT3, ADD PHD zinc finger (DNMT3_ADD_GATA1-like)	DNMT3, ADD PHD zinc finger	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc fin ...	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.	Domain
I [auth P], J [auth Q]	PF17980	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (ADD_DNMT3)	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome ...	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. This domain contains two parts, a GATA1-like and a PHD-like (Pfam:PF21255) zinc fingers. The DNA methyltransferase (DNMT) 3 family members DNMT3A and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development [1,2].	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	PF21255	DNMT3, ADD PHD zinc finger (DNMT3_ADD_GATA1-like)	DNMT3, ADD PHD zinc finger	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc fin ...	DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	PF17980	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (ADD_DNMT3)	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome ...	This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. This domain contains two parts, a GATA1-like and a PHD-like (Pfam:PF21255) zinc fingers. The DNA methyltransferase (DNMT) 3 family members DNMT3A and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development [1,2].	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	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
I [auth P], J [auth Q]	DNA (cytosine-5)-methyltransferase 3-like	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein binding enzyme binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process 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 regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic placenta development animal organ development anatomical structure development methylation extraembryonic membrane development chorion development cellular developmental process cell differentiation chorionic trophoblast cell differentiation epigenetic programming of gene expression epigenetic programming in the zygotic pronuclei epigenetic programing of female pronucleus cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development male meiosis I organelle fission meiotic cell cycle male meiotic nuclear division meiotic cell cycle process nuclear division organelle organization meiosis I meiosis I cell cycle process meiotic nuclear division cell cycle cell cycle process stem cell differentiation multicellular organism development multicellular organismal process post-embryonic development regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation transposable element silencing by piRNA-mediated DNA methylation gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization regulation of cellular component organization positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process positive regulation of cellular process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen cytoplasm cytosol protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex PcG protein complex nucleoplasm methyltransferase complex ESC/E(Z) complex chromatin heterochromatin
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	DNA (cytosine-5)-methyltransferase 3A	RNA binding binding lncRNA binding nucleic acid binding sequence-specific DNA binding DNA binding unmethylated CpG binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity transferase activity methyltransferase activity protein-cysteine methyltransferase activity RNA binding binding lncRNA binding nucleic acid binding sequence-specific DNA binding DNA binding unmethylated CpG binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity transferase activity methyltransferase activity protein-cysteine methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity identical protein binding protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding double-stranded DNA 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 chromatin binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels response to stimulus response to chemical response to xenobiotic stimulus developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus cellular process methylation metabolic process response to nutrient levels response to lipid response to nutrient response to vitamin A response to vitamin response to toxic substance response to ionizing radiation response to radiation cellular response to bisphenol A response to oxygen-containing compound cellular response to oxygen-containing compound response to bisphenol A cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid response to alcohol cellular response to alcohol cellular response to ethanol response to ethanol regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid 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 biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic regulation of cellular response to hypoxia positive regulation of biological process regulation of cellular response to stress positive regulation of response to stimulus regulation of response to stress positive regulation of cellular response to hypoxia positive regulation of cellular process regulation of response to stimulus multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation response to metal ion response to lead ion cell development cellular process involved in reproduction in multicellular organism epigenetic programming of gene expression genomic imprinting autosome genomic imprinting germ cell development hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation post-embryonic development retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing by piRNA-mediated DNA methylation transposable element silencing gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation response to nitrogen compound response to cocaine response to alkaloid response to estradiol	intracellular organelle XY body cellular anatomical structure intracellular anatomical structure sex chromosome organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm chromatin heterochromatin membrane-bounded organelle nucleus intracellular organelle XY body cellular anatomical structure intracellular anatomical structure sex chromosome organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm chromatin heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix chromosome, centromeric region chromosomal region protein-containing complex catalytic complex nucleoplasm euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth P], J [auth Q]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
I [auth P], J [auth Q]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
I [auth P], J [auth Q]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
I [auth P], J [auth Q]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
I [auth P], J [auth Q]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
I [auth P], J [auth Q]	IPR025766	ADD domain	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR000313	PWWP domain	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR001525	C-5 cytosine methyltransferase	Family
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR054724	DNA (cytosine-5)-methyltransferase, N-terminal	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR025766	ADD domain	Domain
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth P], J [auth Q]	Pharos: Q9UJW3	ankylosing spondylitis inflammatory bowel disease ulcerative colitis celiac disease rheumatoid arthritis Crohn disease schizophrenia
A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], A [auth L], B [auth M], C [auth N], D [auth O], E [auth R], F [auth S], G [auth T], H [auth U]	Pharos: Q9Y6K1	tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia acute myeloid leukemia intellectual disability breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia acute myeloid leukemia intellectual disability breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma microcephaly non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic intraductal papillary-mucinous neoplasm genetic endocrine growth disease primary biliary cholangitis ileocolitis systemic mastocytosis atypical teratoid rhabdoid tumor lung cancer malignant ependymoma congenital anemia Crohn's colitis myelodysplastic syndrome oligodendroglioma glioblastoma hematologic disease large cell medulloblastoma autism spectrum disorder malignant glioma osteosarcoma plasma cell myeloma granulomatous slack skin disease primitive neuroectodermal tumor hypertensive disorder invasive ductal breast carcinoma lung benign neoplasm cancer malignant mesothelioma medulloblastoma

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.