8F8Z

PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	FYVE/PHD zinc finger	8067580	3001459	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FYVE/PHD zinc finger	8067580	3001459	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	JmjC_1	e8f8zA3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)
A	KOG1633	e8f8zA2	A: alpha bundles	X: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	H: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	T: C-terminal helical domain in Jumonji domain-containing histone demethylases	F: KOG1633	ECOD (1.6)
A	PHD	e8f8zA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)
B	JmjC_1	e8f8zB3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)
B	KOG1633	e8f8zB1	A: alpha bundles	X: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	H: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	T: C-terminal helical domain in Jumonji domain-containing histone demethylases	F: KOG1633	ECOD (1.6)
B	PHD	e8f8zB2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain
A, B	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, B	Lysine-specific demethylase PHF2	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 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 transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity histone H3K9 demethylase activity histone H3 demethylase activity zinc ion binding methylated histone binding protein binding modification-dependent protein binding histone binding methylation-dependent protein 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 cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process 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 cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular 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 cellular metabolic process biological regulation regulation of cellular metabolic process 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 cellular biosynthetic process 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 positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of heterochromatin formation negative regulation of cellular metabolic process 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 negative regulation of cellular biosynthetic process 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 facultative heterochromatin formation 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 membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome nucleoplasm
C [auth E], D [auth F]	H3 N-Terminal Peptide	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR050690	JHDM1 Histone Demethylase	Family
A, B	IPR003347	JmjC domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR041070	Jumonji, helical domain	Domain
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
C [auth E], D [auth F]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth E], D [auth F]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083
C [auth E], D [auth F]	MLY	Parent Component: LYS RESID: AA0074 , AA0075 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083 , N6,N6-dimethyl-L-lysine MOD:00084

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 R01GM133198.