2PVC | pdb_00002pvc

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]	PHD-1st_NSD	e2pvcB4	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: PHD-1st_NSD	ECOD (v294.1)
C [auth A]	C5HCH	e2pvcA4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: C5HCH	ECOD (v294.1)
E [auth C]	C5HCH	e2pvcC4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: C5HCH	ECOD (v294.1)

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
B [auth D], D [auth E], F	Histone H3 peptide	-	-	-
A [auth B], C [auth A], E [auth C]	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 oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation oocyte development germ cell development oocyte 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 genomic imprinting autosome genomic imprinting 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

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]	IPR050390	DNA Cytosine-5 Methyltransferase	Family
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.