6Y3Z | pdb_00006y3z

Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (Dcp1-Dcp2-Edc3)

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)
C	UNK_F_TYPE	e6y3zC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: UNK_F_TYPE	ECOD (1.6)
A	DCP2	e6y3zA2	A: alpha arrays	X: Dcp2 box A domain (From Topology)	H: Dcp2 box A domain (From Topology)	T: Dcp2 box A domain	F: DCP2	ECOD (1.6)
A	NUDIX_1	e6y3zA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth P]	PF03133	Tubulin-tyrosine ligase family (TTL)	Tubulin-tyrosine ligase family	-	Family
B	PF06058	Dcp1-like decapping family (DCP1)	Dcp1-like decapping family	An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (Pfam:PF05026). The precise role of these proteins in the decapping reaction have not been es ...	An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (Pfam:PF05026). The precise role of these proteins in the decapping reaction have not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2 [1].	Domain
A	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain
A	PF05026	Dcp2, box A domain (DCP2)	Dcp2, box A domain	This domain is always found to the amino terminal side of Pfam:PF00293. This domain is specific to mRNA decapping protein 2 and this region has been termed Box A [2]. Removal of the cap structure is catalysed by the Dcp1-Dcp2 complex [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth P]	Probable tubulin--tyrosine ligase PBY1	acid-amino acid ligase activity catalytic activity, acting on a protein tubulin-tyrosine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding acid-amino acid ligase activity catalytic activity, acting on a protein tubulin-tyrosine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex P-body
C	Enhancer of mRNA-decapping protein 3	RNA binding binding nucleic acid binding mRNA binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to glucose starvation cellular response to starvation regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to glucose starvation cellular response to starvation regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA negative regulation of cellular process mRNA methylguanosine-cap decapping RNA catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-independent decay negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process RNA decapping regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability 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 organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	mRNA-decapping enzyme subunit 1	RNA binding binding nucleic acid binding mRNA binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity	regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process primary metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA regulation of metabolic process RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process mRNA methylguanosine-cap decapping positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 cellular process regulation of mRNA metabolic process deadenylation-independent decapping of nuclear-transcribed mRNA nuclear-transcribed mRNA catabolic process, deadenylation-independent decay nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process 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
A	m7GpppN-mRNA hydrolase	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
D [auth P]	IPR027746	Probable tubulin-tyrosine ligase	Family
D [auth P]	IPR002828	Survival protein SurE-like phosphatase/nucleotidase	Domain
D [auth P]	IPR004344	Tubulin-tyrosine ligase/Tubulin polyglutamylase	Family
D [auth P]	IPR036523	SurE-like phosphatase/nucleotidase superfamily	Homologous Superfamily
D [auth P]	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
C	IPR047575	Sm domain	Domain
C	IPR025762	DFDF domain	Domain
C	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
C	IPR004443	YjeF N-terminal domain	Domain
C	IPR019050	FDF domain	Domain
B	IPR010334	mRNA-decapping enzyme subunit 1	Family
B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR036189	mRNA decapping protein 2, Box A domain superfamily	Homologous Superfamily
A	IPR007722	mRNA decapping protein 2, Box A domain	Domain
A	IPR044099	mRNA decapping enzyme 2 , NUDIX hydrolase domain	Domain
A	IPR000086	NUDIX hydrolase domain	Domain
A	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A	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.