4CUG

Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cupin_4	e4cugA2	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	RoxA	e4cugA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RoxA	ECOD (1.6)
B	Cupin_4	e4cugB2	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	RoxA	e4cugB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RoxA	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	3.40.366.30	Alpha Beta	3-Layer(aba) Sandwich	Malonyl-Coenzyme A Acyl Carrier Protein	domain 2	CATH (4.3.0)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B	3.40.366.30	Alpha Beta	3-Layer(aba) Sandwich	Malonyl-Coenzyme A Acyl Carrier Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20514	ROXA-like winged helix (ROXA-like_wH)	ROXA-like winged helix	This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative char ...	This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids [1].	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	CUPIN 4 FAMILY PROTEIN	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding ion binding binding metal ion binding small molecule binding	-	-
C [auth E], D [auth F]	50S RIBOSOMAL PROTEIN L16	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003347	JmjC domain	Domain
A, B	IPR039994	Histone lysine demethylase/ribosomal histidine hydroxylase NO66-like	Family
A, B	IPR046799	ROXA-like, winged helix	Domain
C [auth E], D [auth F]	IPR036920	Large ribosomal subunit protein uL16 superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR020798	Large ribosomal subunit protein uL16, conserved site	Conserved Site
C [auth E], D [auth F]	IPR000114	Large ribosomal subunit protein uL16, bacterial-type	Family
C [auth E], D [auth F]	IPR016180	Large ribosomal subunit protein uL16 domain	Domain
C [auth E], D [auth F]	IPR047873	Large ribosomal subunit protein uL16	Family

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.