3RSG

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NAD.

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	d3rsga2	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	YjeF C-terminal domain-like	Hypothetical protein TM0922, C-terminal domain	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d3rsga1	Alpha and beta proteins (a/b)	YjeF N-terminal domain-like	YjeF N-terminal domain-like	YjeF N-terminal domain-like	Hypothetical protein TM0922, N-terminal domain	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YjeF N-terminal domain-like	8037443	3000851	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8037442	3001268	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	YjeF_N	e3rsgA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)
A	Carb_kinase	e3rsgA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: Carb_kinase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
A	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01256	NAD(P)H-hydrate dehydratase (Carb_kinase)	NAD(P)H-hydrate dehydratase	Hydration of NAD(P)H to NAD(P)HX, which inhibits several dehydrogenases, is corrected by an ATP-dependent dehydratase and an epimerase. The ATP-dependent dehydratase has been identified as the product of the vertebrate Carkd (carbohydrate kinase do ...	Hydration of NAD(P)H to NAD(P)HX, which inhibits several dehydrogenases, is corrected by an ATP-dependent dehydratase and an epimerase. The ATP-dependent dehydratase has been identified as the product of the vertebrate Carkd (carbohydrate kinase domain) gene [1, 2]. Variants of this enzyme leads to deficient NADHX repair mitochondrial dysfunction in humans, associated with a lethal neurometabolic disorder in early childhood [2]. In E. coli, it is found as the C-terminal domain of a bifunctional enzyme (YjeF) that also includes the epimerase and uses ADP instead of ATP [3]. These enzymes are widespread in eukaryotes, prokaryotes, and archaea.	Domain
A	PF03853	YjeF-related protein N-terminus (YjeF_N)	YjeF-related protein N-terminus	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be ...	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1], where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative uncharacterized protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity ADP-dependent NAD(P)H-hydrate dehydratase activity cation binding metal ion binding isomerase activity NAD(P)HX epimerase activity racemase and epimerase activity	nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process metabolite repair	-
B	Unknown peptide, probably from expression host	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000631	ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase	Domain
A	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
A	IPR017953	Carbohydrate kinase, predicted, conserved site	Conserved Site
A	IPR029056	Ribokinase-like	Homologous Superfamily
A	IPR004443	YjeF N-terminal domain	Domain
A	IPR030677	Bifunctional NAD(P)H-hydrate repair enzyme Nnr	Family

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.