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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pentein	8034757	3000640	SCOP2B (2022-06-29)
A	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)
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)
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)
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)
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
B	3.75.10.20	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (4.3.0)
A	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 amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process L-arginine catabolic process carboxylic acid catabolic process glutamate metabolic process L-arginine catabolic process to L-glutamate small molecule metabolic process amino acid catabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process L-arginine catabolic process carboxylic acid catabolic process glutamate metabolic process L-arginine catabolic process to L-glutamate small molecule metabolic process amino acid catabolic process 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 L-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.