6O3P | pdb_00006o3p

Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	HpcH_HpaI	e6o3pB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: HpcH_HpaI	ECOD (v294.1)
A	NUDIX	e6o3pA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: NUDIX	ECOD (v294.1)
A	HpcH_HpaI	e6o3pA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: HpcH_HpaI	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09296	NADH pyrophosphatase-like rudimentary NUDIX domain (NUDIX-like)	NADH pyrophosphatase-like rudimentary NUDIX domain	The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP.	Domain
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	Peroxisomal NADH pyrophosphatase NUDT12	pyrophosphatase activity NADPH pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NAD+ diphosphatase activity NADH pyrophosphatase activity cation binding magnesium ion binding ion binding binding metal ion binding pyrophosphatase activity NADPH pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NAD+ diphosphatase activity NADH pyrophosphatase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA NAD-cap (NMN-forming) hydrolase activity transition metal ion binding 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 NAD-cap decapping RNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression circadian rhythm biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process mRNA metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process mRNA methylguanosine-cap decapping NAD+ catabolic process NAD+ metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR015375	NADH pyrophosphatase-like, N-terminal	Domain
A, B	IPR015376	Zinc ribbon, NADH pyrophosphatase	Domain
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR002110	Ankyrin repeat	Repeat
A, B	IPR049734	NADH pyrophosphatase-like, C-terminal domain	Domain
A, B	IPR050241	NAD-capped RNA hydrolase NudC subfamily	Family
A, B	IPR000086	NUDIX hydrolase domain	Domain
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.