5BV3 | pdb_00005bv3

Yeast Scavenger Decapping Enzyme in complex with m7GDP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	BON	e5bv3D1	A: alpha bundles	X: Repetitive alpha hairpins	H: C2 domain	T: C2 domain	F: BON	ECOD (develop294)
C	Usher	e5bv3C1	A: alpha bundles	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Usher	ECOD (develop294)
B	YVC1_C	e5bv3B5	A: alpha bundles	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: YVC1_C	ECOD (develop294)
A	Usher	e5bv3A1	A: alpha bundles	X: Inserted helical domain in fatty acid synthase subunit beta	H: Voltage-gated ion channels	T: Voltage-gated ion channels	F: Usher	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
C	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
B	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)
A	3.30.200.40	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	3.30.428.10	Alpha Beta	2-Layer Sandwich	HIT family, subunit A	HIT-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF11969	Scavenger mRNA decapping enzyme C-term binding (DcpS_C)	Scavenger mRNA decapping enzyme C-term binding	-	Family
A, B, C, D	PF05652	Scavenger mRNA decapping enzyme (DcpS) N-terminal (DcpS)	Scavenger mRNA decapping enzyme (DcpS) N-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	m7GpppX diphosphatase	protein heterodimerization activity protein binding binding protein dimerization activity ribonuclease activator activity enzyme regulator activity enzyme activator activity nuclease activator activity molecular function activator activity molecular function regulator activity exoribonuclease activator activity RNA binding RNA 7-methylguanosine cap binding nucleic acid binding protein heterodimerization activity protein binding binding protein dimerization activity ribonuclease activator activity enzyme regulator activity enzyme activator activity nuclease activator activity molecular function activator activity molecular function regulator activity exoribonuclease activator activity RNA binding RNA 7-methylguanosine cap binding nucleic acid binding RNA cap binding identical protein binding protein homodimerization activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity pyrophosphatase activity 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process 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 regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process 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 macromolecule biosynthetic process mRNA metabolic 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 regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 RNA metabolic process deadenylation-dependent decapping of nuclear-transcribed mRNA RNA decapping nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process mRNA methylguanosine-cap decapping 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 nuclear-transcribed mRNA catabolic process, deadenylation-independent decay cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation response to chemical response to nutrient response to oxidative stress response to heat response to abiotic stimulus response to temperature stimulus response to osmotic stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle phosphatase complex protein-containing complex catalytic complex m7G(5')pppN diphosphatase complex perinuclear region of cytoplasm cytoplasmic ribonucleoprotein granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle phosphatase complex protein-containing complex catalytic complex m7G(5')pppN diphosphatase complex perinuclear region of cytoplasm cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex P-body nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011145	Scavenger mRNA decapping enzyme, N-terminal	Homologous Superfamily
A, B, C, D	IPR008594	Scavenger mRNA decapping enzyme DcpS/DCS2	Family
A, B, C, D	IPR019808	Histidine triad, conserved site	Conserved Site
A, B, C, D	IPR036265	HIT-like superfamily	Homologous Superfamily

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.