7OGK

A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. PNPase-3'ETS(leuZ)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8041944	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8041944	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8041944	3000135	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)
B	S1	e7ogkB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
B	PNPase_1	e7ogkB4	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_1	ECOD (1.6)
B	RNase_PH	e7ogkB7	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)
B	RNase_PH_1	e7ogkB6	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)
B	RNase_PH_C_2	e7ogkB3	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)
B	RNase_PH_C	e7ogkB5	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	ECOD (1.6)
B	KH_1_2	e7ogkB2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)
A	S1	e7ogkA7	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
A	PNPase_1	e7ogkA6	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_1	ECOD (1.6)
A	RNase_PH	e7ogkA2	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	e7ogkA3	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	e7ogkA4	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	RNase_PH_C	e7ogkA5	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	ECOD (1.6)
A	KH_1_2	e7ogkA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)
C	S1	e7ogkC6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
C	PNPase_1	e7ogkC1	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_1	ECOD (1.6)
C	RNase_PH	e7ogkC4	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)
C	RNase_PH_1	e7ogkC7	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)
C	RNase_PH_C_2	e7ogkC3	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)
C	RNase_PH_C	e7ogkC5	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	ECOD (1.6)
C	KH_1_2	e7ogkC2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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, B, C	PF03725	3' exoribonuclease family, domain 2 (RNase_PH_C)	3' exoribonuclease family, domain 2	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
A, B, C	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, B, C	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
A, B, C	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, B, C	Polyribonucleotide nucleotidyltransferase	guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding nucleic acid binding cation binding magnesium ion binding metal ion binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups identical protein binding protein binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular 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 metabolic process regulation of macromolecule metabolic process mRNA metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	membrane cellular anatomical entity bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex
D	3'ETS(LeuZ)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR004087	K Homology domain	Domain
A, B, C	IPR012162	Polyribonucleotide nucleotidyltransferase	Family
A, B, C	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A, B, C	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A, B, C	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Homologous Superfamily
A, B, C	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B, C	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
A, B, C	IPR003029	S1 domain	Domain
A, B, C	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Domain
A, B, C	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A, B, C	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A, B, C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C	IPR004088	K Homology domain, type 1	Domain