1OYP | pdb_00001oyp

Crystal Structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis

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)
F	d1oypf1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1oypf2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1oype1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1oype2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1oypd1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1oypd2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1oypc1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1oypc2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1oypb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1oypb2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1oypa1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Ribonuclease PH, domain 1	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1oypa2	Alpha and beta proteins (a+b)	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	Ribonuclease PH, domain 2	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease PH domain 2-like	8037934	3000346	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8037932	3000100	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)
F	Staphylokinase	e1oypF2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
F	KAsynt_C_assoc	e1oypF1	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)
E	Staphylokinase	e1oypE2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
E	KAsynt_C_assoc	e1oypE3	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)
D	Staphylokinase	e1oypD2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
D	KAsynt_C_assoc	e1oypD3	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)
C	Staphylokinase	e1oypC2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
C	KAsynt_C_assoc	e1oypC1	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)
B	Staphylokinase	e1oypB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
B	KAsynt_C_assoc	e1oypB3	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)
A	Staphylokinase	e1oypA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
A	KAsynt_C_assoc	e1oypA1	A: alpha bundles	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: Type II ABC importer transmembrane domain fold	F: KAsynt_C_assoc	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	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)
A	3.30.230.70	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	Ribonuclease PH	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 tRNA binding catalytic activity, acting on a tRNA transferase activity tRNA nucleotidyltransferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process cellular component biogenesis nucleic acid biosynthetic process ribosome biogenesis biosynthetic process rRNA 3'-end processing ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process cellular component biogenesis nucleic acid biosynthetic process ribosome biogenesis biosynthetic process rRNA 3'-end processing RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process cellular component organization or biogenesis rRNA metabolic process tRNA metabolic process tRNA processing catabolic process rRNA catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR050080	Ribonuclease PH	Family
A, B, C, D, E A, B, C, D, E, F	IPR018336	Ribonuclease PH, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002381	Ribonuclease PH, bacterial-type	Family
A, B, C, D, E A, B, C, D, E, F	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain

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.