1E3P | pdb_00001e3p

tungstate derivative of Streptomyces antibioticus PNPase/GPSI enzyme

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1e3pa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	(Streptomyces antibioticus ) [TaxId: 1890 ],	SCOPe (2.08)
A	d1e3pa2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase	(Streptomyces antibioticus ) [TaxId: 1890 ],	SCOPe (2.08)
A	d1e3pa3	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4	(Streptomyces antibioticus ) [TaxId: 1890 ],	SCOPe (2.08)
A	d1e3pa5	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Prokaryotic type KH domain (KH-domain type II)	Prokaryotic type KH domain (KH-domain type II)	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6	(Streptomyces antibioticus ) [TaxId: 1890 ],	SCOPe (2.08)
A	d1e3pa6	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5	(Streptomyces antibioticus ) [TaxId: 1890 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cold shock DNA-binding domain-like	8029566	4001909	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8041945	3000135	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8035885	3000346	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8035882	3000346	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034446	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8034444	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	8036658	3001199	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	HHH_5	e1e3pA2	A: alpha bundles	X: EGF-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (develop294)
A	RF-1	e1e3pA3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: RF-1	ECOD (develop294)
A	Staphylokinase	e1e3pA5	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
A	Lyase_1	e1e3pA7	A: alpha bundles	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (develop294)
A		e1e3pA8	A: alpha bundles	X: DP domain	H: DP domain	T: DP domain	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Polyribonucleotide nucleotidyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity RNA binding nucleic acid binding	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 regulation of biological process negative regulation of metabolic process biological regulation 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 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 nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003029	S1 domain	Domain
A	IPR014069	Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase	Family
A	IPR004087	K Homology domain	Domain
A	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Domain
A	IPR012162	Polyribonucleotide nucleotidyltransferase	Family
A	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Homologous Superfamily
A	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR004088	K Homology domain, type 1	Domain

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.