2GB5 | pdb_00002gb5

Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 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)
B	d2gb5b1	Alpha and beta proteins (a+b)	Nudix	Nudix	NADH pyrophosphatase	NADH pyrophosphatase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2gb5b2	Small proteins	Rubredoxin-like	NADH pyrophosphatase intervening domain	NADH pyrophosphatase intervening domain	NADH pyrophosphatase intervening domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2gb5b4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2gb5a1	Alpha and beta proteins (a+b)	Nudix	Nudix	NADH pyrophosphatase	NADH pyrophosphatase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2gb5a2	Small proteins	Rubredoxin-like	NADH pyrophosphatase intervening domain	NADH pyrophosphatase intervening domain	NADH pyrophosphatase intervening domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2gb5a4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nudix	8042152	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NADH pyrophosphatase intervening domain	8042153	3001752	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8036012	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8036012	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NADH pyrophosphatase intervening domain	8042153	3001752	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8042152	3000098	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)
B	ABC_tran	e2gb5B1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: ABC_tran	ECOD (v294.1)
A	B12-binding	e2gb5A1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: B12-binding	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.79.20	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase		CATH (4.3.0)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	3.90.79.20	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase		CATH (4.3.0)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09297	NADH pyrophosphatase zinc ribbon domain (Zn_ribbon_NUD)	NADH pyrophosphatase zinc ribbon domain	This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.	Domain
A, B	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NADH pyrophosphatase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA NAD-cap (NMN-forming) hydrolase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA NAD-cap (NMN-forming) hydrolase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity manganese ion binding transition metal ion binding NAD+ diphosphatase activity dinucleotide phosphatase activity NADH pyrophosphatase activity zinc ion binding	pyridine nucleotide catabolic process catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyridine nucleotide catabolic process catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process purine nucleotide catabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process NADP+ metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organophosphate metabolic process NADP+ catabolic process metabolic process cellular process pyridine-containing compound catabolic process regulation of cellular process negative regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process NAD+ catabolic process NAD+ metabolic process NAD-cap decapping RNA decapping positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality mRNA stabilization negative regulation of RNA metabolic process positive regulation of biological process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process positive regulation of cellular process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process regulation of mRNA stability RNA stabilization positive regulation of gene expression regulation of RNA stability regulation of mRNA metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049734	NADH pyrophosphatase-like, C-terminal domain	Domain
A, B	IPR022925	NAD-capped RNA hydrolase NudC	Family
A, B	IPR050241	NAD-capped RNA hydrolase NudC subfamily	Family
A, B	IPR000086	NUDIX hydrolase domain	Domain
A, B	IPR015376	Zinc ribbon, NADH pyrophosphatase	Domain
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

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.