4AID

Crystal structure of C. crescentus PNPase bound to RNase E recognition peptide

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	e4aidA9	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	e4aidA8	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	e4aidA6	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	PNPase_KH,RNase_PH_C_2	e4aidA7	A: a+b two layers	X: Ribonuclease PH domain 2-like	H: Ribonuclease PH domain 2 (From Topology)	T: Ribonuclease PH domain 2	F: PNPase_KH,RNase_PH_C_2	ECOD (1.6)
A	RNase_PH_C	e4aidA4	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	e4aidB14	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	e4aidB13	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	e4aidB11	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	e4aidB12	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	e4aidB15	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	e4aidC1	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	e4aidC6	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	e4aidC3	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	e4aidC4	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	e4aidC5	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)
A	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)
B	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)
C	1.10.10.400	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

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.