2A8S

2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP

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	d2a8sa_	Alpha and beta proteins (a+b)	Nudix	Nudix	MutT-like	automated matches	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d2a8sb_	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	e2a8sA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)
B	NUDIX_3	e2a8sB1	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	PF22327	U8 snoRNA-decapping enzyme-like (Nudt16-like)	U8 snoRNA-decapping enzyme-like	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later report ...	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later reported to be specialised in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. It adopts a canonical NUDIX fold, an alpha-beta-alpha sandwich constituted by two beta-sheets whose strands interact in a way that could also be described as a single extended beta-sheet [1].	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 RNA NAD+-cap (NAD+-forming) hydrolase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid nucleoside phosphate binding nucleotide binding heterocyclic compound binding manganese ion binding magnesium ion binding mRNA binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA nuclease 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 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 deoxyribose phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process deoxyribonucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process deoxyribonucleotide catabolic process 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 deoxyribose phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process deoxyribonucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process deoxyribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process carbohydrate derivative catabolic process cellular metabolic process 2'-deoxyribonucleotide metabolic process primary metabolic process purine-containing compound catabolic process deoxyribonucleoside triphosphate catabolic process nucleotide metabolic process deoxyribose phosphate metabolic process dITP metabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process dITP catabolic process purine deoxyribonucleotide metabolic process metabolic process cellular process nucleoside triphosphate metabolic process NAD-cap decapping RNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping ribonucleoprotein complex biogenesis regulation of cellular process negative regulation of biological process regulation of ribosome biogenesis negative regulation of cellular metabolic process regulation of primary metabolic process cellular component biogenesis ribosome biogenesis regulation of RNA metabolic 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 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 RNA biosynthetic process nucleic acid biosynthetic process 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 nucleobase-containing compound biosynthetic process regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process macromolecule catabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleic acid catabolic process sno(s)RNA metabolic 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
A, B	IPR051894	Nudix_hydrolase_NUDT16_sf	Unknown

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.