8F8Y

PHF2 (PHD+JMJ) in Complex with VRK1 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	PF02373	e8f8yA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF02373	ECOD (1.6)
A	PF17811	e8f8yA2	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: PF17811	ECOD (1.6)
A	PF00628	e8f8yA3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF00628	ECOD (1.6)
B	PF02373	e8f8yB3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF02373	ECOD (1.6)
B	PF17811	e8f8yB1	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: PF17811	ECOD (1.6)
B	PF00628	e8f8yB2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF00628	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 positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of 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 positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II chromatin organization organic substance biosynthetic process positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biological process cellular metabolic process regulation of cellular metabolic process primary metabolic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process chromatin remodeling cellular component organization or biogenesis positive regulation of cellular process regulation of biosynthetic process protein-containing complex organization epigenetic regulation of gene expression biological regulation 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 positive regulation of gene expression cellular 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 organonitrogen compound metabolic process 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]	Serine/threonine-protein kinase VRK1 N-terminus peptide	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding histone binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding histone binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase binding enzyme binding protein kinase binding protein serine/threonine kinase activity histone H3T3 kinase activity histone H3 kinase activity histone modifying activity histone kinase activity histone H3S10 kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component disassembly Golgi inheritance organelle inheritance Golgi disassembly cellular component organization organelle organization organelle disassembly cellular component organization or biogenesis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component disassembly Golgi inheritance organelle inheritance Golgi disassembly cellular component organization organelle organization organelle disassembly cellular component organization or biogenesis Golgi organization endomembrane system organization cell division membrane organization nuclear membrane disassembly mitotic cell cycle membrane disassembly nuclear membrane organization mitotic nuclear membrane disassembly nucleus organization mitotic cell cycle process nuclear envelope organization cell cycle cell cycle process regulation of biological process regulation of cellular process signaling biological regulation signal transduction cell communication protein phosphorylation organonitrogen compound metabolic process protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process protein localization regulation of localization cellular localization protein localization to chromatin regulation of protein localization positive regulation of biological process localization protein localization to chromosome regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization positive regulation of protein localization to chromatin regulation of protein localization to chromatin positive regulation of cellular 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 Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system Golgi stack cytoplasm cytosol nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
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]	IPR017441	Protein kinase, ATP binding site	Binding Site
C [auth E], D [auth F]	IPR000719	Protein kinase domain	Domain
C [auth E], D [auth F]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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
C [auth E], D [auth F]	Pharos: Q99986	intellectual disability pontocerebellar hypoplasia type 1A pontocerebellar hypoplasia pontocerebellar hypoplasia type 1 acute myeloid leukemia Cerebellar Hypoplasia lung cancer neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor lymphoplasmacytic lymphoma oligodendroglioma pituitary cancer large cell medulloblastoma medulloblastoma intellectual disability pontocerebellar hypoplasia type 1A pontocerebellar hypoplasia pontocerebellar hypoplasia type 1 acute myeloid leukemia Cerebellar Hypoplasia lung cancer neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor lymphoplasmacytic lymphoma oligodendroglioma pituitary cancer large cell medulloblastoma medulloblastoma microcephaly pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma

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

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.