5YU0 | pdb_00005yu0

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

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	d5yu0a_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
B	d5yu0b_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
C	d5yu0c_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)
D	d5yu0d_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Streptomyces pristinaespiralis ) [TaxId: 38300 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ornithine cyclodeaminase-like	8063737	4000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8063738	3000041	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	OCD_Mu_crystall_N	e5yu0A1	A: a+b two layers	X: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	H: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	T: Ornithine cyclodeaminase-like enzymes dimerization domain	F: OCD_Mu_crystall_N	ECOD (1.6)
A	OCD_Mu_crystall_C	e5yu0A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)
B	OCD_Mu_crystall_N	e5yu0B1	A: a+b two layers	X: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	H: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	T: Ornithine cyclodeaminase-like enzymes dimerization domain	F: OCD_Mu_crystall_N	ECOD (1.6)
B	OCD_Mu_crystall_C	e5yu0B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)
C	OCD_Mu_crystall_N	e5yu0C2	A: a+b two layers	X: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	H: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	T: Ornithine cyclodeaminase-like enzymes dimerization domain	F: OCD_Mu_crystall_N	ECOD (1.6)
C	OCD_Mu_crystall_C	e5yu0C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)
D	OCD_Mu_crystall_N	e5yu0D1	A: a+b two layers	X: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	H: Ornithine cyclodeaminase-like enzymes dimerization domain (From Topology)	T: Ornithine cyclodeaminase-like enzymes dimerization domain	F: OCD_Mu_crystall_N	ECOD (1.6)
D	OCD_Mu_crystall_C	e5yu0D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02423	Ornithine cyclodeaminase/mu-crystallin family (OCD_Mu_crystall)	Ornithine cyclodeaminase/mu-crystallin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lysine cyclodeaminase	ornithine cyclodeaminase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR003462	Ornithine cyclodeaminase/mu-crystallin	Family
A, B, C, D	IPR023401	Ornithine cyclodeaminase, N-terminal	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.