1E3H

SeMet 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
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	d1e3ha1	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	d1e3ha2	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	d1e3ha4	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	d1e3ha5	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	Ribonuclease PH domain 1-like	8022064	4000958	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribonuclease PH domain 1-like	8022066	4000958	SCOP2 (2022-06-29)
A	SCOP2 Family	Prokaryotic type KH domain (KH-domain type II)	8022729	4001200	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribonuclease PH domain 2-like	8023502	4001767	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribonuclease PH domain 2-like	8023505	4001767	SCOP2 (2022-06-29)
A	SCOP2 Family	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	8024279	4000738	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8034444	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8034446	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prokaryotic type KH domain (KH-domain type II)	8035109	3001043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease PH domain 2-like	8035882	3000346	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease PH domain 2-like	8035885	3000346	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	8036658	3001199	SCOP2 (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	PNPase	e1e3hA1	A: alpha arrays	X: HTH	H: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 (From Topology)	T: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	F: PNPase	ECOD (1.6)
A	RNase_PH	e1e3hA5	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: RNase_PH	ECOD (1.6)
A	RNase_PH_1	e1e3hA6	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: RNase_PH_1	ECOD (1.6)
A	RNase_PH_C_2	e1e3hA2	A: a+b two layers	X: Ribonuclease PH domain 2-like	H: Ribonuclease PH domain 2 (From Topology)	T: Ribonuclease PH domain 2	F: RNase_PH_C_2	ECOD (1.6)
A	pppGpp_PNP_like	e1e3hA4	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: pppGpp_PNP_like	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03726	Polyribonucleotide nucleotidyltransferase, RNA binding domain (PNPase)	Polyribonucleotide nucleotidyltransferase, RNA binding domain	This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction.	Domain
A	PF00013	KH domain (KH_1)	KH domain	KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.	Domain
A	PF01138	3' exoribonuclease family, domain 1 (RNase_PH)	3' exoribonuclease family, domain 1	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of ...	This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain [1]. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GUANOSINE PENTAPHOSPHATE SYNTHETASE	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 RNA binding organic cyclic compound binding nucleic acid binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic 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	intracellular anatomical structure cytoplasm cellular anatomical entity

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.