Annotations: 3U1K

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PNPase	e3u1kA2	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	e3u1kA5	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	e3u1kA4	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	e3u1kA3	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	e3u1kA1	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	e3u1kA6	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)
B [auth C]	PNPase	e3u1kC3	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)
B [auth C]	RNase_PH	e3u1kC1	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 [auth C]	RNase_PH_1	e3u1kC5	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 [auth C]	RNase_PH_C_2	e3u1kC4	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 [auth C]	RNase_PH_C	e3u1kC2	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 [auth C]	KH_1_2	e3u1kC6	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 [auth B]	PNPase	e3u1kB5	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)
C [auth B]	RNase_PH	e3u1kB4	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 [auth B]	RNase_PH_1	e3u1kB1	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 [auth B]	RNase_PH_C_2	e3u1kB2	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 [auth B]	RNase_PH_C	e3u1kB3	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 [auth B]	KH_1_2	e3u1kB6	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)
D	PNPase	e3u1kD2	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)
D	RNase_PH	e3u1kD3	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)
D	RNase_PH_1	e3u1kD5	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)
D	RNase_PH_C_2	e3u1kD1	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)
D	RNase_PH_C	e3u1kD4	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)
D	KH_1_2	e3u1kD6	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)
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)
A	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B [auth C]	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B [auth C]	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)
B [auth C]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C [auth B]	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C [auth B]	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)
C [auth B]	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
D	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)
D	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth B], D	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 [auth C], C [auth B], D	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 [auth C], C [auth B], D	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 [auth C], C [auth B], D	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 [auth C], C [auth B], D	Polyribonucleotide nucleotidyltransferase 1, mitochondrial	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 identical protein 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 identical protein binding protein binding binding RNA binding organic cyclic compound binding nucleic acid binding regulatory RNA binding miRNA binding poly(G) binding poly-purine tract binding single-stranded RNA binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups poly-pyrimidine tract binding poly(U) RNA binding	cellular response to stimulus regulation of biological process regulation of cellular process regulation of cellular senescence response to stimulus cellular metabolic process biological regulation cellular senescence regulation of cellular metabolic process cellular response to stress response to stress cellular process metabolic process regulation of metabolic process cellular response to stimulus regulation of biological process regulation of cellular process regulation of cellular senescence response to stimulus cellular metabolic process biological regulation cellular senescence regulation of cellular metabolic process cellular response to stress response to stress cellular process metabolic process regulation of metabolic process RNA transport nitrogen compound transport transport organic substance transport nucleic acid transport mitochondrial transmembrane transport establishment of localization transmembrane transport localization import into the mitochondrion RNA import into mitochondrion establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport mitochondrial transport cellular biosynthetic process RNA metabolic process primary metabolic process gene expression mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process macromolecule metabolic process RNA processing response to interferon-beta response to organic substance response to cytokine cellular response to interferon-beta cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance catabolic process positive regulation of biological process positive regulation of miRNA metabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of miRNA catabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process RNA catabolic process positive regulation of nucleobase-containing compound metabolic process regulation of macromolecule metabolic process regulation of catabolic process miRNA catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process positive regulation of catabolic process positive regulation of RNA metabolic process ncRNA metabolic process nucleic acid catabolic process positive regulation of miRNA catabolic process organic substance catabolic process response to oxidative stress cellular response to oxidative stress cellular response to chemical stress response to growth hormone response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to oxygen-containing compound response to nitrogen compound response to organophosphorus response to purine-containing compound response to cAMP response to organic cyclic compound protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis regulation of growth negative regulation of growth negative regulation of biological process growth positive regulation of mitochondrial RNA catabolic process regulation of mitochondrial RNA catabolic process mitochondrial RNA catabolic process mitochondrial RNA metabolic process negative regulation of cellular metabolic process mRNA catabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular biosynthetic process positive regulation of mRNA catabolic process negative regulation of biosynthetic process regulation of mRNA metabolic process rRNA import into mitochondrion rRNA transport mitochondrial mRNA catabolic process developmental process multicellular organismal process gland development animal organ development animal organ regeneration liver development regeneration multicellular organism development hepaticobiliary system development anatomical structure development liver regeneration system development mitochondrial gene expression mitochondrial RNA processing RNA 3'-end processing mitochondrial RNA 3'-end processing post-transcriptional regulation of gene expression nuclear polyadenylation-dependent mRNA catabolic process regulation of biological quality polyadenylation-dependent mRNA catabolic process mRNA destabilization RNA destabilization regulation of mRNA stability regulation of RNA stability cell cycle regulation of cell cycle mitochondrial RNA 5'-end processing RNA 5'-end processing organelle organization mitochondrion organization cellular respiration energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration tRNA processing mitochondrial tRNA processing mitochondrial mRNA polyadenylation tRNA metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex mitochondrion intracellular membrane-bounded organelle cytoplasmic exosome (RNase complex) intracellular organelle exosome (RNase complex) mitochondrial degradosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex mitochondrion intracellular membrane-bounded organelle cytoplasmic exosome (RNase complex) intracellular organelle exosome (RNase complex) mitochondrial degradosome organelle exoribonuclease complex mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen mitochondrial envelope intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C], C [auth B], D	Pharos: Q8TCS8	autosomal recessive nonsyndromic deafness 70 combined oxidative phosphorylation defect type 13 nonsyndromic genetic deafness Pick disease hepatocellular carcinoma juvenile dermatomyositis metabolic syndrome X non-small cell lung carcinoma osteosarcoma progressive supranuclear palsy breast cancer combined oxidative phosphorylation deficiency intellectual disability Leigh syndrome Mitochondrial Diseases autosomal recessive nonsyndromic deafness 70 combined oxidative phosphorylation defect type 13 nonsyndromic genetic deafness Pick disease hepatocellular carcinoma juvenile dermatomyositis metabolic syndrome X non-small cell lung carcinoma osteosarcoma progressive supranuclear palsy breast cancer combined oxidative phosphorylation deficiency intellectual disability Leigh syndrome Mitochondrial Diseases ovarian cancer vitiligo carpal tunnel syndrome Hashimoto thyroiditis invasive ductal breast carcinoma nasopharyngeal carcinoma open-angle glaucoma