6O3P

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)
A	PF00293	e6o3pA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
A	PF09296	e6o3pA2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF09296	ECOD (1.6)
A	PF09297	e6o3pA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF09297	ECOD (1.6)
B	PF00293	e6o3pB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF00293	ECOD (1.6)
B	PF09296	e6o3pB2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: PF09296	ECOD (1.6)
B	PF09297	e6o3pB3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF09297	ECOD (1.6)

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 (zf-NADH-PPase)	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	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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity pyrophosphatase activity RNA NAD-cap (NMN-forming) hydrolase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides NAD+ diphosphatase activity dinucleotide phosphatase activity NADH pyrophosphatase activity transition metal ion binding zinc ion binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process 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 metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process NAD-cap decapping RNA decapping nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process nucleotide metabolic process NAD metabolic process NADH metabolic process purine-containing compound metabolic process purine nucleotide metabolic process organophosphate 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 pyridine nucleotide metabolic process pyridine nucleotide catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleotide catabolic process organonitrogen compound catabolic process purine nucleotide catabolic process purine-containing compound catabolic process NADP catabolic process NADP metabolic process pyridine-containing compound catabolic process NAD catabolic process mRNA methylguanosine-cap decapping rhythmic process circadian regulation of gene expression circadian rhythm	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002110	Ankyrin repeat	Repeat
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR015375	NADH pyrophosphatase-like, N-terminal	Domain
A, B	IPR049734	NADH pyrophosphatase-like, Nudix hydrolase C-terminal domain	Domain
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 R01GM133198.