4KG3 | pdb_00004kg3

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	RNase_H	e4kg3A1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: RNase_H	ECOD (v294.1)
B		e4kg3B1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F:	ECOD (v294.1)
C	RNase_H	e4kg3C1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: RNase_H	ECOD (v294.1)

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 nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding chromatin binding hydrolase activity catalytic activity pyrophosphatase activity RNA binding binding nucleic acid binding mRNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule 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 DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic 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 positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic 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 positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of transcription initiation by RNA polymerase II biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process negative regulation of biological 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 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 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 cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay nuclear-transcribed mRNA catabolic process, nonsense-mediated decay mRNA processing RNA processing	cellular anatomical structure cytoplasmic side of membrane membrane side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm cellular anatomical structure cytoplasmic side of membrane membrane side of membrane protein-containing complex RNA decapping complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm supramolecular complex P-body 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 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.