2PNZ | pdb_00002pnz

Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2pnzb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
B	d2pnzb2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	automated matches	automated matches	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d2pnza1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d2pnza2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	automated matches	automated matches	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	RNase_PH_2	e2pnzB3	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_2	ECOD (1.6)
B	RNase_PH_C_1	e2pnzB4	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_1	ECOD (1.6)
A	RNase_PH	e2pnzA2	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_C_3	e2pnzA1	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_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.2.0)
A	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Probable exosome complex exonuclease 2	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 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	exosome (RNase complex) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm cytoplasmic exosome (RNase complex) exoribonuclease complex
A	Probable exosome complex exonuclease 1	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 nucleic acid binding	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 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 biosynthetic process gene expression macromolecule biosynthetic process	exosome (RNase complex) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm cytoplasmic exosome (RNase complex) exoribonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
B	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
B	IPR050590	Exosome complex component Rrp42 subfamily	Family
B	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B	IPR020869	Exosome complex component Rrp42, archaea	Family
A	IPR011807	Exosome complex component Rrp41	Family
A	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
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
A	IPR050080	Ribonuclease PH	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.