3GME

Crystal Structure of Polynucleotide Phosphorylase in complex with RNase E and manganese

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)
A	PNPase_1	e3gmeA2	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_1	ECOD (1.6)
A	RNase_PH	e3gmeA3	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	e3gmeA1	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	e3gmeA5	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	e3gmeA4	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)
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	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	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 [auth D]	PF12111	Polyribonucleotide phosphorylase C terminal (PNPase_C)	Polyribonucleotide phosphorylase C terminal	PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-fac ...	PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C terminal protomer domain of the PNPase core. The function of the C terminal protomer is to catalyse phosphorolysis through its two active sites. [1]	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 RNA binding organic cyclic compound binding nucleic acid binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process organic substance biosynthetic process RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process cellular nitrogen compound metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process organic substance biosynthetic process RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process aromatic compound catabolic process negative regulation of cellular biosynthetic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process heterocycle catabolic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process catabolic process cellular biosynthetic process RNA metabolic process macromolecule catabolic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process organic substance catabolic process cellular aromatic compound metabolic process RNA processing	intracellular anatomical structure cytoplasm cellular anatomical entity
B [auth D]	Ribonuclease E	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding organic cyclic compound binding rRNA binding nucleic acid binding endonuclease activity RNA endonuclease activity transition metal ion binding zinc ion binding tRNA binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process organic substance biosynthetic process RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process cellular nitrogen compound metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process cellular catabolic process heterocycle metabolic process organic substance biosynthetic process RNA catabolic process mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process aromatic compound catabolic process negative regulation of cellular biosynthetic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process heterocycle catabolic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process catabolic process cellular biosynthetic process RNA metabolic process macromolecule catabolic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process organic substance catabolic process cellular aromatic compound metabolic process ribonucleoprotein complex biogenesis rRNA processing ncRNA processing cellular component biogenesis ribosome biogenesis RNA processing cellular component organization or biogenesis rRNA metabolic process ncRNA metabolic process tRNA processing tRNA metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003029	S1 domain	Domain
A	IPR004087	K Homology domain	Domain
A	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Domain
A	IPR012162	Polyribonucleotide nucleotidyltransferase	Family
A	IPR027408	PNPase/RNase PH domain superfamily	Homologous Superfamily
A	IPR001247	Exoribonuclease, phosphorolytic domain 1	Domain
A	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Homologous Superfamily
A	IPR036345	Exoribonuclease, PH domain 2 superfamily	Homologous Superfamily
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR004088	K Homology domain, type 1	Domain
A	IPR015847	Exoribonuclease, phosphorolytic domain 2	Domain
B [auth D]	IPR028878	Ribonuclease E	Family
B [auth D]	IPR003029	S1 domain	Domain
B [auth D]	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G	Family
B [auth D]	IPR004659	Ribonuclease E/G	Family
B [auth D]	IPR021968	Polyribonucleotide phosphorylase C-terminal	Domain
B [auth D]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B [auth D]	IPR048583	RNase E/G, thioredoxin-like domain	Domain