4Y3O

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine

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	Cupin_4	e4y3oA2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_4	ECOD (1.6)
A	KOG3706	e4y3oA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG3706	ECOD (1.6)
B	Cupin_4	e4y3oB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_4	ECOD (1.6)
B	KOG3706	e4y3oB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG3706	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	1.10.10.1500	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	JmjC domain-containing ribosomal oxygenase (ROX), dimer domain	CATH (4.3.0)
A	3.90.930.40	Alpha Beta	Alpha-Beta Complex	Outer Surface Protein A	domain 3	CATH (4.3.0)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B	1.10.10.1500	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	JmjC domain-containing ribosomal oxygenase (ROX), dimer domain	CATH (4.3.0)
B	3.90.930.40	Alpha Beta	Alpha-Beta Complex	Outer Surface Protein A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21233	Ribosomal oxygenase 1, C-terminal winged helix domain (RIOX1_C_WH)	Ribosomal oxygenase 1, C-terminal winged helix domain	This domain is found in Ribosomal oxygenase 1 from humans (RIOX1) and similar proteins from animals. RIOX1 catalyse histidine- hydroxylation in ribosomal protein rpL28. The protein shows a JmjC domain followed by an helical dimerization domain and a ...	This domain is found in Ribosomal oxygenase 1 from humans (RIOX1) and similar proteins from animals. RIOX1 catalyse histidine- hydroxylation in ribosomal protein rpL28. The protein shows a JmjC domain followed by an helical dimerization domain and a C-terminal winged-helix (WH)-domain (this entry) [1,2].	Domain
A, B	PF08007	JmjC domain (JmjC_2)	JmjC domain	This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1], Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase fro ...	This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 [1], Ribosomal oxygenase 1/2 [2,3], and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli [4,5]. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66	histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K4 demethylase activity histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity histone H3K4 demethylase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity peptidyl-histidine dioxygenase activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic 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 regulation of osteoblast differentiation multicellular organismal process regulation of developmental process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification cell differentiation negative regulation of cell differentiation	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 nucleoplasm
C, D	Rpl8 peptide	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	cellular biosynthetic process cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane intracellular organelle intracellular anatomical structure cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytoplasm cytosol anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane intracellular organelle intracellular anatomical structure cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytoplasm cytosol non-membrane-bounded organelle postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse asymmetric synapse protein-containing complex ribosomal subunit cytosolic large ribosomal subunit ribonucleoprotein complex large ribosomal subunit membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049043	RIOX1/NO66-like, C-terminal winged helix domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR039994	Histone lysine demethylase/ribosomal histidine hydroxylase NO66-like	Family
C, D	IPR022669	Large ribosomal subunit protein uL2, C-terminal	Domain
C, D	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
C, D	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
C, D	IPR023672	Large ribosomal subunit protein uL2, archaeal-type	Family
C, D	IPR022671	Large ribosomal subunit protein uL2, conserved site	Conserved Site
C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C, D	IPR022666	Large ribosomal subunit protein uL2, RNA-binding domain	Domain
C, D	IPR014726	Large ribosomal subunit protein uL2, domain 3	Homologous Superfamily
C, D	IPR002171	Large ribosomal subunit protein uL2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9H6W3	astrocytic tumor osteosarcoma lung cancer oligodendroglioma

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.