2HBJ

Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2hbja1	All alpha proteins	SAM domain-like	HRDC-like	EXOSC10 HRDC domain-like	Exosome complex exonuclease RRP6 domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2hbja2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exosome complex exonuclease RRP6	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2hbja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	HRDC-like	8042226	3000132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8042228	3000143	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	PF00570	e2hbjA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00570	ECOD (1.6)
A	PF01612	e2hbjA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF01612	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01612	3'-5' exonuclease (DNA_pol_A_exo1)	3'-5' exonuclease	This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the ...	This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [4,5]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein [3]. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.	Domain
A	PF00570	HRDC domain (HRDC)	HRDC domain	The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains ...	The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Exosome complex exonuclease RRP6	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding single-stranded RNA 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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding nucleic acid binding single-stranded RNA 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 rRNA primary transcript binding rRNA binding	catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process cellular catabolic process organic substance metabolic process heterocycle metabolic process nuclear polyadenylation-dependent ncRNA catabolic process modification-dependent macromolecule catabolic process sno(s)RNA metabolic process nitrogen compound metabolic process RNA surveillance polyadenylation-dependent ncRNA catabolic process RNA catabolic process catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process cellular catabolic process organic substance metabolic process heterocycle metabolic process nuclear polyadenylation-dependent ncRNA catabolic process modification-dependent macromolecule catabolic process sno(s)RNA metabolic process nitrogen compound metabolic process RNA surveillance polyadenylation-dependent ncRNA catabolic process RNA catabolic process nuclear RNA surveillance nuclear ncRNA surveillance cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process aromatic compound catabolic process nucleic acid metabolic process cellular nitrogen compound catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process ncRNA catabolic process organic cyclic compound metabolic process ncRNA metabolic process polyadenylation-dependent RNA catabolic process heterocycle catabolic process metabolic process cellular process macromolecule metabolic process sno(s)RNA catabolic process organic substance catabolic process cellular aromatic compound metabolic process nuclear polyadenylation-dependent snoRNA catabolic process cellular biosynthetic process ncRNA processing organic substance biosynthetic process RNA 3'-end processing RNA processing sno(s)RNA processing polyadenylation-dependent snoRNA 3'-end processing gene expression macromolecule biosynthetic process sno(s)RNA 3'-end processing biosynthetic process snRNA metabolic process snRNA processing U5 snRNA 3'-end processing snRNA 3'-end processing nuclear polyadenylation-dependent antisense transcript catabolic process antisense RNA transcript catabolic process antisense RNA metabolic process CUT metabolic process CUT catabolic process nuclear polyadenylation-dependent CUT catabolic 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 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 polyadenylation-dependent snRNA catabolic process snRNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular 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 metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process U4 snRNA 3'-end processing histone mRNA metabolic process histone mRNA catabolic process nuclear polyadenylation-dependent tRNA catabolic process tRNA surveillance tRNA catabolic process tRNA metabolic process rRNA catabolic process nuclear polyadenylation-dependent rRNA catabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process nuclear polyadenylation-dependent mRNA catabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process polyadenylation-dependent mRNA catabolic process positive regulation of biological process positive regulation of cellular metabolic process mRNA destabilization regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of nitrogen compound metabolic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of mRNA metabolic process cellular component organization organelle organization chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery U1 snRNA 3'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex nuclear protein-containing complex nuclear exosome (RNase complex)

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR002121	HRDC domain	Domain
A	IPR012588	Exosome-associated factor Rrp6, N-terminal	Domain
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR045092	Exosome complex exonuclease Rrp6-like	Family
A	IPR002562	3'-5' exonuclease domain	Domain
A	IPR049559	Rrp6-like, 3'-5' exonuclease domain	Domain
A	IPR010997	HRDC-like superfamily	Homologous Superfamily
A	IPR044876	HRDC domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.