2PVC

DNMT3L recognizes unmethylated histone H3 lysine 4

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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 [auth B]	DNA_methylase_1	e2pvcB6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
A [auth B]	ADDz_Dnmt3l	e2pvcB5	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3l	ECOD (1.6)
A [auth B]	ADDz_Dnmt3b	e2pvcB4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3b	ECOD (1.6)
C [auth A]	DNA_methylase_1	e2pvcA6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
C [auth A]	ADDz_Dnmt3l	e2pvcA5	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3l	ECOD (1.6)
C [auth A]	ADDz_Dnmt3b	e2pvcA4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3b	ECOD (1.6)
E [auth C]	DNA_methylase_1	e2pvcC6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
E [auth C]	ADDz_Dnmt3l	e2pvcC5	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3l	ECOD (1.6)
E [auth C]	ADDz_Dnmt3b	e2pvcC4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: ADDz_Dnmt3b	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C [auth A]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
E [auth C]	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 [auth B], C [auth A], E [auth C]	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 B], C [auth A], E [auth C]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], C [auth A], E [auth C]	DNA (cytosine-5)-methyltransferase 3-like	DNA binding binding organic cyclic compound 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 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA binding binding organic cyclic compound 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 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding enzyme binding cation binding ion binding metal ion binding small molecule binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation placenta development animal organ development anatomical structure development methylation metabolic process extraembryonic membrane development developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation placenta development animal organ development anatomical structure development methylation metabolic process extraembryonic membrane development chorion development cellular developmental process cell differentiation chorionic trophoblast cell differentiation cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic 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 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 macromolecule metabolic process regulation of metabolic process DNA methylation-dependent heterochromatin formation heterochromatin formation constitutive heterochromatin formation epigenetic programming in the zygotic pronuclei epigenetic programing of female pronucleus epigenetic programming of gene expression cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development retrotransposon silencing retrotransposon silencing by heterochromatin formation retrotransposition transposition 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 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 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process stem cell differentiation 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 DNA methylation-dependent heterochromatin formation regulation of cellular component organization positive regulation of biological process positive regulation of cellular metabolic process negative regulation of chromatin organization positive regulation of biosynthetic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle condensed chromosome non-membrane-bounded organelle 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
B [auth D], D [auth E], F	Histone H3 peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], C [auth A], E [auth C]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A [auth B], C [auth A], E [auth C]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A [auth B], C [auth A], E [auth C]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth B], C [auth A], E [auth C]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A [auth B], C [auth A], E [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth B], C [auth A], E [auth C]	IPR025766	ADD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], C [auth A], E [auth C]	Pharos: Q9UJW3	ankylosing spondylitis inflammatory bowel disease ulcerative colitis celiac disease rheumatoid arthritis Crohn disease schizophrenia

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.