3PU8 | pdb_00003pu8

PHF2 Jumonji-NOG-Fe(II) complex

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 [auth A]	d3pu8a_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Jumonji domain / Histone demethylase core	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth B]	d3pu8b_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Jumonji domain / Histone demethylase core	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	JHD	e3pu8A1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: JHD	ECOD (v294.1)
A [auth B]	JHD	e3pu8B1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: JHD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B [auth A]	1.20.58.1360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A [auth B]	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A [auth B]	1.20.58.1360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A]	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain
A [auth B], B [auth A]	PF17811	Jumonji helical domain (JHD)	Jumonji helical domain	This 4-helix bundle domain is associated with the Jumonji domain Pfam:PF02373 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A]	PHD finger protein 2	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity transcription regulator activity transcription coregulator activity transcription coactivator activity histone H4 demethylase activity catalytic activity, acting on a protein protein demethylase activity histone H4K20 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity transcription regulator activity transcription coregulator activity transcription coactivator activity histone H4 demethylase activity catalytic activity, acting on a protein protein demethylase activity histone H4K20 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding histone H3K9 demethylase activity histone H3 demethylase activity zinc ion binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of biological process negative regulation of heterochromatin formation cellular component biogenesis cellular component assembly regulation of rDNA heterochromatin formation rDNA heterochromatin formation regulation of heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleolus organization negative regulation of gene expression, epigenetic regulation of cellular component organization nucleolar chromatin organization negative regulation of chromatin organization negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of rDNA heterochromatin formation nucleus organization organelle organization negative regulation of biosynthetic process regulation of heterochromatin organization facultative heterochromatin formation negative regulation of heterochromatin organization regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription protein dealkylation protein demethylation macromolecule modification demethylation protein metabolic process protein modification process	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 nucleoplasm chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR001965	Zinc finger, PHD-type	Domain
A [auth B], B [auth A]	IPR003347	JmjC domain	Domain
A [auth B], B [auth A]	IPR041070	Jumonji, helical domain	Domain
A [auth B], B [auth A]	IPR019787	Zinc finger, PHD-finger	Domain
A [auth B], B [auth A]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A [auth B], B [auth A]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A [auth B], B [auth A]	IPR050690	JHDM1 Histone Demethylase	Family
A [auth B], B [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth A]	Pharos: O75151	Neurodevelopmental Disorders astrocytic tumor malignant mesothelioma osteosarcoma endogenous depression medulloblastoma subependymal giant cell astrocytoma lung adenocarcinoma

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.