5YJ2 | pdb_00005yj2

Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5yj2d1	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	Urate oxidase (uricase)	automated matches	(Bacillus sp. TB-90 ) [TaxId: 36824 ],	SCOPe (2.08)
C	d5yj2c1	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	Urate oxidase (uricase)	automated matches	(Bacillus sp. TB-90 ) [TaxId: 36824 ],	SCOPe (2.08)
B	d5yj2b1	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	Urate oxidase (uricase)	automated matches	(Bacillus sp. TB-90 ) [TaxId: 36824 ],	SCOPe (2.08)
A	d5yj2a1	Alpha and beta proteins (a+b)	T-fold	Tetrahydrobiopterin biosynthesis enzymes-like	Urate oxidase (uricase)	automated matches	(Bacillus sp. TB-90 ) [TaxId: 36824 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037883	3000283	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037881	3000283	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037881	3000283	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037883	3000283	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037883	3000283	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037881	3000283	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037881	3000283	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tetrahydrobiopterin biosynthesis enzymes-like	8037883	3000283	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)
D	Uricase	e5yj2D2	A: a+b two layers	X: T-fold	H: Tetrahydrobiopterin biosynthesis enzymes-like (From Topology)	T: Tetrahydrobiopterin biosynthesis enzymes-like	F: Uricase	ECOD (1.6)
C	Uricase	e5yj2C2	A: a+b two layers	X: T-fold	H: Tetrahydrobiopterin biosynthesis enzymes-like (From Topology)	T: Tetrahydrobiopterin biosynthesis enzymes-like	F: Uricase	ECOD (1.6)
B	Uricase	e5yj2B2	A: a+b two layers	X: T-fold	H: Tetrahydrobiopterin biosynthesis enzymes-like (From Topology)	T: Tetrahydrobiopterin biosynthesis enzymes-like	F: Uricase	ECOD (1.6)
A	Uricase	e5yj2A1	A: a+b two layers	X: T-fold	H: Tetrahydrobiopterin biosynthesis enzymes-like (From Topology)	T: Tetrahydrobiopterin biosynthesis enzymes-like	F: Uricase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.270.10	Alpha Beta	Roll	Urate Oxidase	Urate Oxidase	CATH (4.3.0)
C	3.10.270.10	Alpha Beta	Roll	Urate Oxidase	Urate Oxidase	CATH (4.3.0)
B	3.10.270.10	Alpha Beta	Roll	Urate Oxidase	Urate Oxidase	CATH (4.3.0)
A	3.10.270.10	Alpha Beta	Roll	Urate Oxidase	Urate Oxidase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01014	Uricase (Uricase)	Uricase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Uric acid degradation bifunctional protein	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity oxidoreductase activity urate oxidase activity oxidoreductase activity, acting on other nitrogenous compounds as donors oxidoreductase activity, acting on other nitrogenous compounds as donors, oxygen as acceptor	catabolic process urate catabolic process small molecule metabolic process metabolic process cellular process purine-containing compound catabolic process small molecule catabolic process purine-containing compound metabolic process urate metabolic process allantoin metabolic process amide metabolic process nucleobase-containing compound metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process catabolic process urate catabolic process small molecule metabolic process metabolic process cellular process purine-containing compound catabolic process small molecule catabolic process purine-containing compound metabolic process urate metabolic process allantoin metabolic process amide metabolic process nucleobase-containing compound metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process primary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019842	Uricase, conserved site	Conserved Site
A, B, C, D	IPR036778	Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily	Homologous Superfamily
A, B, C, D	IPR002042	Uricase	Family
A, B, C, D	IPR017580	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1	Domain
A, B, C, D	IPR018020	Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

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.