1YNF | pdb_00001ynf

Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli

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	d1ynfa1	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	Succinylarginine dihydrolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ynfb_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ynfc_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ynfd_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1ynfe_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1ynff_	Alpha and beta proteins (a+b)	Pentein, beta/alpha-propeller	Pentein	Succinylarginine dihydrolase-like	automated matches	(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	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Pentein	8034757	3000640	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	AstB	e1ynfA1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)
B	AstB	e1ynfB1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)
C	AstB	e1ynfC1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)
D	AstB	e1ynfD1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)
E	AstB	e1ynfE1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)
F	AstB	e1ynfF1	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: AstB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
B	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
C	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
D	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
E	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
F	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF04996	Succinylarginine dihydrolase (AstB)	Succinylarginine dihydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Succinylarginine dihydrolase	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity N-succinylarginine dihydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process arginine catabolic process to glutamate dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process succinate metabolic process arginine catabolic process to succinate	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR007079	Succinylarginine dihydrolase	Family
A, B, C, D, E A, B, C, D, E, F	IPR037031	Succinylarginine dihydrolase superfamily	Homologous Superfamily

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.