4LIT

Structure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate.

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	e4litA1	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	e4litA2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	50S ribosomal protein L16 arginine hydroxylase	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity	macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003347	JmjC domain	Domain
A	IPR039994	Histone lysine demethylase/ribosomal histidine hydroxylase NO66-like	Family
A	IPR046799	ROXA-like, winged helix	Domain

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.