3NIO | pdb_00003nio

Crystal structure of Pseudomonas aeruginosa guanidinobutyrase

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)
F	d3niof_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
E	d3nioe_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
D	d3niod_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C	d3nioc_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B	d3niob_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
A	d3nioa_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2B (2022-06-29)
A	SCOP2 Family	Arginase-like amidino hydrolases	8076536	4000424	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8076537	3000260	SCOP2 (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	Flavin_Reduct	e3nioF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
E	Flavin_Reduct	e3nioE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
D	Flavin_Reduct	e3nioD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
C	Flavin_Reduct	e3nioC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
B	Flavin_Reduct	e3nioB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
A	NAD_binding_10	e3nioA1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: NAD_binding_10	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
B	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
A	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	Guanidinobutyrase	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 guanidinobutyrase activity	oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine metabolic process small molecule metabolic process carboxylic acid metabolic process primary metabolic process polyamine metabolic process putrescine biosynthetic process from arginine, via agmatine L-amino acid metabolic process putrescine biosynthetic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine metabolic process small molecule metabolic process carboxylic acid metabolic process primary metabolic process polyamine metabolic process putrescine biosynthetic process from arginine, via agmatine L-amino acid metabolic process putrescine biosynthetic process amine metabolic process proteinogenic amino acid metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine biosynthetic process from arginine metabolic process cellular process biogenic amine metabolic process catabolic process L-amino acid catabolic process organic acid catabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR005925	Agmatinase-related	Family
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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.