3RPH | pdb_00003rph

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+.

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	d3rpha1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	YjeF C-terminal domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d3rpha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribokinase-like	8040759	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	MR_MLE_C	e3rphA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: MR_MLE_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ADP/ATP-dependent NAD(P)H-hydrate dehydratase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 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 metabolite repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000631	ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase	Domain
A	IPR017953	Carbohydrate kinase, predicted, conserved site	Conserved Site
A	IPR029056	Ribokinase-like	Homologous Superfamily

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.