4KG3

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q mutation)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d4kg3a_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4kg3b_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d4kg3c_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	NUDIX_1	e4kg3A1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
B	NUDIX_1	e4kg3B1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
C	NUDIX_1	e4kg3C1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	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)
C	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, C	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, C	mRNA-decapping enzyme subunit 2	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding protein-containing complex binding chromatin binding hydrolase activity RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding protein-containing complex binding chromatin binding hydrolase activity catalytic activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of transcription initiation by RNA polymerase II biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression regulation of biological quality RNA catabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping negative regulation of macromolecule metabolic process nuclear-transcribed mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process organic cyclic compound catabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly non-membrane-bounded organelle assembly cellular component organization or biogenesis nuclear-transcribed mRNA catabolic process, deadenylation-independent decay deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, nonsense-mediated decay mRNA processing RNA processing	cytoplasmic side of membrane membrane cellular anatomical entity side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex cytoplasmic side of membrane membrane cellular anatomical entity side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex P-body non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR036189	mRNA decapping protein 2, Box A domain superfamily	Homologous Superfamily
A, B, C	IPR007722	mRNA decapping protein 2, Box A domain	Domain
A, B, C	IPR044099	mRNA decapping enzyme 2 , NUDIX hydrolase domain	Domain
A, B, C	IPR000086	NUDIX hydrolase domain	Domain
A, B, C	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

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.