1WOH

Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily

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	d1woha1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
A	d1woha2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1wohb1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B	d1wohb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1wohc1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C	d1wohc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1wohd1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
D	d1wohd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
E	d1wohe1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
E	d1wohe2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
F	d1wohf1	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Agmatinase	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
F	d1wohf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Arginase-like amidino hydrolases	8029400	4000424	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8041779	3000260	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8041779	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8041779	3000260	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8041779	3000260	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Arginase/deacetylase-like	8041779	3000260	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Arginase/deacetylase-like	8041779	3000260	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	Arginase	e1wohA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
B	Arginase	e1wohB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
C	Arginase	e1wohC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
D	Arginase	e1wohD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
E	Arginase	e1wohE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
F	Arginase	e1wohF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
B	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
C	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
D	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
E	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
F	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	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	PF00491	Arginase family (Arginase)	Arginase family	-	Domain

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	agmatinase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity agmatinase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	oxoacid metabolic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine biosynthetic process from arginine, using agmatinase organic substance metabolic process organic substance biosynthetic process putrescine metabolic process small molecule metabolic process organonitrogen compound metabolic process cellular metabolic process oxoacid metabolic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine biosynthetic process from arginine, using agmatinase organic substance metabolic process organic substance biosynthetic process putrescine metabolic process small molecule metabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process polyamine metabolic process putrescine biosynthetic process amine metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine biosynthetic process from arginine metabolic process cellular process biogenic amine metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR020855	Ureohydrolase, manganese-binding site	Binding Site
A, B, C, D, E A, B, C, D, E, F	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006035	Ureohydrolase	Family

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.