2WP8 | pdb_00002wp8

yeast rrp44 nuclease

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)
B	d2wp8b1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2wp8b2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	automated matches	automated matches	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth J]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037618	3000135	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037616	3000135	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037614	3000135	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037617	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	PNPase	e2wp8A3	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PNPase	ECOD (develop294)
B	RbsD_FucU	e2wp8B1	A: alpha bundles	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: RbsD_FucU	ECOD (develop294)
C [auth J]	Glycolytic	e2wp8J1	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Glycolytic	ECOD (develop294)
C [auth J]	DNA_pack_C	e2wp8J5	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: DNA_pack_C	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)
B	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C [auth J]	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
C [auth J]	2.40.50.700	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C [auth J]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
B	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
B	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
C [auth J]	PF17849	Dis3-like cold-shock domain 2 (CSD2) (OB_Dis3)	Dis3-like cold-shock domain 2 (CSD2)	This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA.	Domain
C [auth J]	PF13638	PIN domain (PIN_4)	PIN domain	Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).	Domain
C [auth J]	PF17215	S1 domain (Rrp44_S1)	S1 domain	This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44 [1].	Domain
C [auth J]	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	EXOSOME COMPLEX COMPONENT RRP45	mRNA 3'-UTR binding RNA binding mRNA 3'-UTR AU-rich region binding binding nucleic acid binding mRNA binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process nuclear RNA surveillance RNA surveillance catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process nuclear RNA surveillance RNA surveillance nuclear polyadenylation-dependent rRNA catabolic process gene expression nucleobase-containing compound biosynthetic process U5 snRNA 3'-end processing macromolecule biosynthetic process snRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process biosynthetic process snRNA processing RNA 3'-end processing RNA processing rRNA catabolic process rRNA metabolic process ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 3'-end processing 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 nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process nuclear mRNA surveillance 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 U4 snRNA 3'-end processing U1 snRNA 3'-end processing tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex nuclear protein-containing complex nuclear exosome (RNase complex) cytoplasm cytoplasmic exosome (RNase complex)
B	EXOSOME COMPLEX COMPONENT SKI6	RNA binding 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 nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process 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 nuclear-transcribed 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 U5 snRNA 3'-end processing snRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process snRNA metabolic process snRNA processing RNA 3'-end processing RNA processing nuclear RNA surveillance nuclear polyadenylation-dependent CUT catabolic process CUT catabolic process RNA surveillance ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process maturation of 5.8S rRNA maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA 3'-end processing nuclear mRNA surveillance U4 snRNA 3'-end processing nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process poly(A)-dependent snoRNA 3'-end processing rRNA catabolic process U1 snRNA 3'-end processing tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex cytoplasm cytoplasmic exosome (RNase complex) nuclear protein-containing complex nuclear exosome (RNase complex)
C [auth J]	EXOSOME COMPLEX EXONUCLEASE DIS3	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 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 binding tRNA binding nucleic acid binding endonuclease activity RNA endonuclease activity	nonfunctional rRNA decay catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process nonfunctional rRNA decay catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process nuclear RNA surveillance nuclear polyadenylation-dependent CUT catabolic process CUT catabolic process RNA surveillance ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process RNA 3'-end processing cellular component organization or biogenesis RNA processing maturation of 5.8S rRNA gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process rRNA 3'-end processing 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 nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process nuclear mRNA surveillance 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 mRNA processing nuclear mRNA surveillance of mRNA 3'-end processing nuclear polyadenylation-dependent rRNA catabolic process regulatory ncRNA 3'-end processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex cytoplasmic exosome (RNase complex) nuclear protein-containing complex nuclear exosome (RNase complex)

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR033100	Exosome complex component RRP45	Family
A	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A	IPR050590	Exosome complex component Rrp42 subfamily	Family
A	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B	IPR050080	Ribonuclease PH	Family
B	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
B	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
C [auth J]	IPR050180	RNR Ribonuclease	Family
C [auth J]	IPR041505	Dis3-like cold-shock domain 2	Domain
C [auth J]	IPR003029	S1 domain	Domain
C [auth J]	IPR022966	Ribonuclease II/R, conserved site	Conserved Site
C [auth J]	IPR033770	Exosome complex exonuclease RRP44, S1 domain	Domain
C [auth J]	IPR033771	Rrp44-like cold shock domain	Domain
C [auth J]	IPR002716	PIN domain	Domain
C [auth J]	IPR001900	Ribonuclease II/R	Domain
C [auth J]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
C [auth J]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily