1J5P

Crystal structure of aspartate dehydrogenase (TM1643) from Thermotoga maritima at 1.9 A resolution

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	d1j5pa4	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Hypothetical protein TM1643	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1j5pa3	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Hypothetical protein TM1643	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1j5pa5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Dihydrodipicolinate reductase-like	8058459	4000095	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8058460	3000043	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	DUF108	e1j5pA1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DUF108	ECOD (1.6)
A	DapB_N	e1j5pA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_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 (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01958	Aspartate dehydrogenase, C-terminal (Asp_DH_C)	Aspartate dehydrogenase, C-terminal	This entry represents the C-terminal domain of aspartate dehydrogenases that belong to a unique class of amino acid dehydrogenases. The structure of Thermotoga maritima TM1643 has been found to contain an N-terminal Rossmann fold domain (which binds ...	This entry represents the C-terminal domain of aspartate dehydrogenases that belong to a unique class of amino acid dehydrogenases. The structure of Thermotoga maritima TM1643 has been found to contain an N-terminal Rossmann fold domain (which binds the NAD(P)+ cofactor) and a C-terminal alpha/beta domain [1]. Enzymatic characterisation of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward L-aspartate but no aspartate oxidase activity [1]. Members of this group share some structural similarity to several other NAD(P)+-dependent oxidoreductases, including inositol 1-phosphate synthase, dihydrodipicolinate reductase, and ASA-DH [1]. It has been proposed that in Thermotoga maritima, TM1643 catalyses the first reaction of de novo biosynthesis of NAD from aspartate, and it produces iminoaspartate required for this pathway.	Domain
A	PF03447	Homoserine dehydrogenase, NAD binding domain (NAD_binding_3)	Homoserine dehydrogenase, NAD binding domain	This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ASPARTATE DEHYDROGENASE	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity aspartate dehydrogenase activity	nucleotide biosynthetic process organonitrogen compound biosynthetic process NAD metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process NAD metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process NAD biosynthetic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process cellular metabolic process pyridine-containing compound biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process organic cyclic compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR011182	L-aspartate dehydrogenase	Family
A	IPR002811	Aspartate dehydrogenase	Domain
A	IPR005106	Aspartate/homoserine dehydrogenase, NAD-binding	Domain
A	IPR022487	L-aspartate dehydrogenase, archaeal	Family
A	IPR020626	L-aspartate dehydrogenase, prokaryotic	Family

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.