1X7D | pdb_00001x7d

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1x7da_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Ornithine cyclodeaminase-like	Ornithine cyclodeaminase	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d1x7db_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Ornithine cyclodeaminase-like	Ornithine cyclodeaminase	(Pseudomonas putida ) [TaxId: 303 ],	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	8000866	4000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ornithine cyclodeaminase-like	8000867	3000041	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ornithine cyclodeaminase-like	8000867	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		e1x7dA3	A: jelly-roll	X: Zn-dependent exopeptidases	H: Zn-dependent exopeptidases	T:	F:	ECOD (20:10:01)
B		e1x7dB1	A: Ribonuclease H-like	X: Ribonuclease H-like	H: Ribonuclease H-like	T: HLH	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1780.10	Alpha Beta	2-Layer Sandwich	ornithine cyclodeaminase, domain 1	ornithine cyclodeaminase, domain 1	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.1780.10	Alpha Beta	2-Layer Sandwich	ornithine cyclodeaminase, domain 1	ornithine cyclodeaminase, domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	ornithine 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	oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process L-proline metabolic process metabolic process cellular process small molecule metabolic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	ornithine cyclodeaminase M-CSA #717	Ornithine cyclodeaminase (OCD) from Pseudomonas putida belongs to the mu-crystallin protein family. It catalyses the conversion of L-ornithine to L-proline by an NAD+ dependent hydride transfer reaction. The precise function of this protein is still unknown, but it may have a regulatory function in the use of amino acids as neurotransmitters.	Defined by 2 residues: GLU:A-56ASP:A-228 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.3.1.12 (PDB Primary Data) Search M-CSA Motif + EC 4.3.1.12

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.

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