7OGM | pdb_00007ogm

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

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth K]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
B [auth J]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
H [auth N]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041944	3000135	SCOP2B (2022-06-29)
I [auth O]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041944	3000135	SCOP2B (2022-06-29)
G [auth L]	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)
A [auth K]	LSM	e7ogmK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B [auth J]	LSM	e7ogmJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C [auth I]	LSM	e7ogmI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e7ogmE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e7ogmF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e7ogmD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H [auth N]	S1	e7ogmN4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
H [auth N]	PNPase_1	e7ogmN5	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)
H [auth N]	RNase_PH	e7ogmN1	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)
H [auth N]	RNase_PH_1	e7ogmN6	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)
H [auth N]	RNase_PH_C_2	e7ogmN2	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)
H [auth N]	RNase_PH_C	e7ogmN7	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)
H [auth N]	KH_1_2	e7ogmN3	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)
I [auth O]	S1	e7ogmO3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
I [auth O]	PNPase_1	e7ogmO2	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)
I [auth O]	RNase_PH	e7ogmO6	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)
I [auth O]	RNase_PH_1	e7ogmO1	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)
I [auth O]	RNase_PH_C_2	e7ogmO7	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)
I [auth O]	RNase_PH_C	e7ogmO5	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)
I [auth O]	KH_1_2	e7ogmO4	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)
G [auth L]	S1	e7ogmL3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1	ECOD (1.6)
G [auth L]	PNPase_1	e7ogmL4	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)
G [auth L]	RNase_PH	e7ogmL2	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)
G [auth L]	RNase_PH_1	e7ogmL5	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)
G [auth L]	RNase_PH_C_2	e7ogmL6	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)
G [auth L]	RNase_PH_C	e7ogmL1	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)
G [auth L]	KH_1_2	e7ogmL7	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth N]	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
H [auth N]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (utative)
I [auth O]	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
I [auth O]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (utative)
G [auth L]	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
G [auth L]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (utative)
G [auth L]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth K], B [auth J], C [auth I], D, E, A [auth K], B [auth J], C [auth I], D, E, F	PF17209	Hfq protein (Hfq)	Hfq protein		Domain
G [auth L], H [auth N], I [auth O]	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
G [auth L], H [auth N], I [auth O]	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
G [auth L], H [auth N], I [auth O]	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
G [auth L], H [auth N], I [auth O]	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
G [auth L], H [auth N], I [auth O]	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 [auth K], B [auth J], C [auth I], D, E, A [auth K], B [auth J], C [auth I], D, E, F	RNA-binding protein Hfq	DNA binding bent DNA binding binding nucleic acid 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 DNA binding bent DNA binding binding nucleic acid 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 RNA binding tRNA binding RNA folding chaperone	regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of translation, ncRNA-mediated positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process translation positive regulation of translation, ncRNA-mediated positive regulation of gene expression regulation of translation tRNA metabolic process tRNA processing RNA processing negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process sRNA-mediated post-transcriptional gene silencing negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing	intracellular organelle bacterial nucleoid cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle nucleoid cytoplasm cytosol
G [auth L], H [auth N], I [auth O]	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 anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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 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	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 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 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 macromolecule metabolic process mRNA metabolic 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	cellular anatomical structure membrane bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex
J [auth P]	3'ETS(LeuZ)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth K], B [auth J], C [auth I], D, E, A [auth K], B [auth J], C [auth I], D, E, F	IPR005001	RNA-binding protein Hfq	Family
A [auth K], B [auth J], C [auth I], D, E, A [auth K], B [auth J], C [auth I], D, E, F	IPR047575	Sm domain	Domain
A [auth K], B [auth J], C [auth I], D, E, A [auth K], B [auth J], C [auth I], D, E, F	IPR010920	LSM domain superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR004087	K Homology domain	Domain
G [auth L], H [auth N], I [auth O]	IPR012162	Polyribonucleotide nucleotidyltransferase	Family
G [auth L], H [auth N], I [auth O]	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
G [auth L], H [auth N], I [auth O]	IPR003029	S1 domain	Domain
G [auth L], H [auth N], I [auth O]	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Domain
G [auth L], H [auth N], I [auth O]	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
G [auth L], H [auth N], I [auth O]	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G [auth L], H [auth N], I [auth O]	IPR004088	K Homology domain, type 1	Domain