1W28

Conformational flexibility of the C-terminus with implications for substrate binding and catalysis in a new crystal form of deacetoxycephalosporin C synthase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w28a_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Penicillin synthase-like	Deacetoxycephalosporin C synthase	(Streptomyces clavuligerus ) [TaxId: 1901 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Clavaminate synthase-like	8043052	3001848	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	DIOX_N	e1w28A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: DIOX_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.330	Mainly Beta	Sandwich	Jelly Rolls	B-lactam Antibiotic, Isopenicillin N Synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03171	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reacti ...	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DEACETOXYCEPHALOSPORIN C SYNTHASE	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen deacetoxycephalosporin-C synthase activity catalytic activity organic acid binding binding carbohydrate binding vitamin binding ion binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen deacetoxycephalosporin-C synthase activity catalytic activity organic acid binding binding carbohydrate binding vitamin binding ion binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity cation binding transition metal ion binding iron ion binding metal ion binding	antibiotic metabolic process biosynthetic process metabolic process antibiotic biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A	IPR050231	Iron/ascorbate-dependent oxidoreductase	Family
A	IPR002057	Isopenicillin N synthase, conserved site	Conserved Site
A	IPR027443	Isopenicillin N synthase-like superfamily	Homologous Superfamily
A	IPR044861	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	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.