3NYE

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Arginine

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e3nyeA2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01266	e3nyeA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF01266	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	D-Arginine Dehydrogenase	oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH2 group of donors D-amino-acid dehydrogenase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process arginine metabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process arginine metabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006076	FAD dependent oxidoreductase	Domain
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	D-arginine dehydrogenase M-CSA #978	D-arginine dehydrogenase (DADH) is a flavin-dependent oxidoreductase. It is a member of the structural family consisting of D-amino acid oxidase, sarcosine oxidase, dimethyl glycine oxidase, and glycine oxidase. The enzyme has broad substrate specificity towards D-amino acids, particularly with cationic and hydrophobic D-amino acids. DADH and L-arginine dehydrogenase (LADH) make up a two-enzyme system involved in D- to L-arginine racemisation in pseudomonads and related species and both enzymes are products of the dauBAR operon, by D-arginine and D-lysine. Crystallographic data shows that DADH from Pseudomonas aeruginosa (PaDADH) contains an active site loop L1 with two flexible segments that span the FAD-binding site and the substrate-binding site. It can occupy two distinct conformations, an open conformation competent for substrate binding and a closed conformation which is catalytically relevant and ligand-bound.	Defined by 6 residues: SER:A-51 [auth A-1045]ALA:A-52 [auth A-1046]HIS:A-54 [auth A-1048]TYR:A-59 [auth A-1053]GLU:A-93 [auth A-1087]TYR:A-255 [auth A-1249] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.4.1 (PDB Primary Data) Search M-CSA Motif + EC 1.4.1

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.