1RC6

Crystal structure of protein Ylba from E. coli, Pfam DUF861

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	d1rc6a_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	YlbA-like	Hypothetical protein YlbA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1rc6b_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	YlbA-like	Hypothetical protein YlbA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	AllE-like	8028113	4000965	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RmlC-like cupins	8040492	3001825	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8040492	3001825	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	Cupin_3	e1rc6A3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_3	ECOD (1.6)
A	Cupin_2	e1rc6A2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_2	ECOD (1.6)
B	Cupin_3	e1rc6B3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_3	ECOD (1.6)
B	Cupin_2	e1rc6B2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: Cupin_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07883	Cupin domain (Cupin_2)	Cupin domain	This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel).	Domain
A, B	PF05899	EutQ-like cupin domain (Cupin_3)	EutQ-like cupin domain	This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is ...	This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity [1]. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins [2]. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It catalyses the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine [3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical protein ylbA	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding ureidoglycine aminohydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	organonitrogen compound metabolic process purine nucleobase metabolic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR044704	(S)-ureidoglycine aminohydrolase, N-terminal cupin domain	Domain
A, B	IPR044697	(S)-ureidoglycine aminohydrolase, C-terminal cupin domain	Domain
A, B	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B	IPR017627	(S)-ureidoglycine aminohydrolase	Family
A, B	IPR013096	Cupin 2, conserved barrel	Domain
A, B	IPR008579	(S)-ureidoglycine aminohydrolase, cupin domain	Domain
A, B	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.