1BG6 | pdb_00001bg6

CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C

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	d1bg6a1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	N-(1-D-carboxylethyl)-L-norvaline dehydrogenase	N-(1-D-carboxylethyl)-L-norvaline dehydrogenase	(Arthrobacter sp. 1C ) [TaxId: 79670 ],	SCOPe (2.08)
A	d1bg6a2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	N-(1-D-carboxylethyl)-L-norvaline dehydrogenase	(Arthrobacter sp. 1C ) [TaxId: 79670 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Opine dehydrogenase (ODH)-like	8001163	4000110	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8001164	3000048	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)
A	Octopine_DH	e1bg6A1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: Octopine_DH	ECOD (1.6)
A	NAD_Gly3P_dh_N	e1bg6A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_Gly3P_dh_N	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 (4.2.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02317	NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain (Octopine_DH)	NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids.	Domain
A	PF02558	Ketopantoate reductase PanE/ApbA (ApbA)	Ketopantoate reductase PanE/ApbA	This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopanto ...	This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway [2]. ApbA and PanE are allelic [2]. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE	opine dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A	IPR003421	Opine dehydrogenase	Domain
A	IPR051729	Opine/Lysopine Dehydrogenase	Family
A	IPR013332	Ketopantoate reductase, N-terminal domain	Domain
A	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	opine dehydrogenase M-CSA #617	N-(1-D-carboxylethyl)-L-norvaline dehydrogenase is part of the (D,L) stereochemistry family of opine dehydrogenases and is able to catalyse the reaction of pyruvate with hydrophobic L amino acids to form opines through reductive condensation using NAD(P)H as a cofactor. Of particular interest is the stereochemical specificity of this enzyme as its reaction is a key step in a number of synthetic routes for pharmaceuticals. The enzyme displays some sequence homology with (L,L) opine dehydrogenases and both families display homology with 2-hydroxy acid dehydrogenases.	Defined by 2 residues: HIS:A-202ASP:A-297 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.5.1.28 (UniProt) Search M-CSA Motif + EC 1.5.1.28

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.