2A8P

2.7 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2a8pa_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d2a8pb_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nudix	8032716	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8032716	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)
A	NUDIX_3	e2a8pA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)
B	NUDIX_3	e2a8pB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	U8 snoRNA-binding protein X29	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding RNA binding organic cyclic compound binding snoRNA binding nucleic acid binding pyrophosphatase activity dITP diphosphatase activity nucleoside triphosphate diphosphatase activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding RNA binding organic cyclic compound binding snoRNA binding nucleic acid binding pyrophosphatase activity dITP diphosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding manganese ion binding magnesium ion binding mRNA binding identical protein binding protein binding protein homodimerization activity protein dimerization activity RNA NAD+-cap (NAD+-forming) hydrolase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid dIDP phosphatase activity nucleoside diphosphate phosphatase activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity exopeptidase activity metalloexopeptidase activity 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity IDP phosphatase activity	deoxyribonucleotide catabolic process nucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process purine deoxyribonucleoside triphosphate catabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process deoxyribonucleotide catabolic process nucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process purine deoxyribonucleoside triphosphate catabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process deoxyribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process purine deoxyribonucleotide catabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process purine-containing compound catabolic process aromatic compound catabolic process deoxyribonucleoside triphosphate catabolic process nucleotide metabolic process dITP metabolic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process purine deoxyribonucleotide metabolic process heterocycle catabolic process metabolic process nucleoside triphosphate metabolic process catabolic process deoxyribose phosphate catabolic process organic substance metabolic process purine nucleotide metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process nitrogen compound metabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process organic cyclic compound catabolic process purine-containing compound metabolic process organophosphate metabolic process dITP catabolic process cellular process organic substance catabolic process cellular aromatic compound metabolic process RNA metabolic process nucleic acid metabolic process NAD-cap decapping macromolecule metabolic process RNA decapping ribonucleoprotein complex biogenesis regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process regulation of ribosome biogenesis negative regulation of cellular metabolic process regulation of primary metabolic process ncRNA processing regulation of nitrogen compound metabolic process cellular component biogenesis ribosome biogenesis regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process regulation of rRNA processing negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process negative regulation of ribosome biogenesis regulation of metabolic process negative regulation of rRNA processing negative regulation of RNA metabolic process cellular biosynthetic process rRNA processing negative regulation of cellular process cellular component organization or biogenesis rRNA metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process ncRNA metabolic process RNA catabolic process mRNA catabolic process macromolecule catabolic process mRNA metabolic process sno(s)RNA metabolic process ncRNA catabolic process sno(s)RNA catabolic process regulation of cell cycle process positive regulation of biological process positive regulation of cell cycle positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR000086	NUDIX hydrolase domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.