4E2S | pdb_00004e2s

Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine

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)
P	d4e2sp_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
O	d4e2so_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
N	d4e2sn_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
M	d4e2sm_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
L	d4e2sl_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
K	d4e2sk_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
J	d4e2sj_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
I	d4e2si_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
H	d4e2sh_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
G	d4e2sg_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d4e2sf_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d4e2se_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d4e2sd_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4e2sc_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4e2sb_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4e2sa_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8083127	3001825	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RmlC-like cupins	8083127	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)
P		e4e2sP1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
O		e4e2sO1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
N		e4e2sN1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
M		e4e2sM1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
L		e4e2sL1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
K		e4e2sK1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
J		e4e2sJ1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
I		e4e2sI1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
H		e4e2sH1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
G		e4e2sG1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
F		e4e2sF1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
E		e4e2sE1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
D		e4e2sD1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
C		e4e2sC1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
B		e4e2sB1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
A		e4e2sA1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
O	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
N	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
M	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
L	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
K	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
J	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
I	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
H	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
G	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
F	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
E	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
D	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C	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)
A	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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	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

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, G, H, I, J, K, L, M, N, O, P	Ureidoglycine aminohydrolase	transcription regulator activity DNA-binding transcription factor activity 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 cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process allantoin metabolic process catabolic process allantoin catabolic process purine nucleobase metabolic process purine-containing compound catabolic process purine nucleobase catabolic process purine-containing compound metabolic process nucleobase catabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process ureide catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR044704	(S)-ureidoglycine aminohydrolase, N-terminal cupin domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR044697	(S)-ureidoglycine aminohydrolase, C-terminal cupin domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR017627	(S)-ureidoglycine aminohydrolase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR013096	Cupin 2, conserved barrel	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR011051	RmlC-like cupin domain 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.