5XEX | pdb_00005xex

Crystal structure of S.aureus PNPase catalytic domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	PNPase	e5xexF4	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)
F	RNase_PH	e5xexF1	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)
F	RNase_PH_1	e5xexF3	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)
F	RNase_PH_C_2	e5xexF5	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)
F	RNase_PH_C	e5xexF2	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)
E	PNPase	e5xexE4	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)
E	RNase_PH	e5xexE2	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)
E	RNase_PH_1	e5xexE1	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)
E	RNase_PH_C_2	e5xexE5	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)
E	RNase_PH_C	e5xexE3	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	PNPase	e5xexD3	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	e5xexD5	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	e5xexD2	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	e5xexD4	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	e5xexD1	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	PNPase	e5xexC2	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	RNase_PH	e5xexC1	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	RNase_PH_1	e5xexC3	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	RNase_PH_C_2	e5xexC4	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	RNase_PH_C	e5xexC5	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	PNPase	e5xexB4	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	RNase_PH	e5xexB1	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	RNase_PH_1	e5xexB5	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	RNase_PH_C_2	e5xexB2	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	RNase_PH_C	e5xexB3	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	PNPase	e5xexA5	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	e5xexA4	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	e5xexA1	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	e5xexA2	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	e5xexA3	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)

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	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, 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	Polyribonucleotide nucleotidyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding polyribonucleotide nucleotidyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 RNA binding nucleic acid 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 regulation of cellular process negative regulation of biological process 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 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 regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003029	S1 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004087	K Homology domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR012162	Polyribonucleotide nucleotidyltransferase	Family
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	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Homologous Superfamily
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	IPR012340	Nucleic acid-binding, OB-fold	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	IPR004088	K Homology domain, type 1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain