4AID | pdb_00004aid

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		e4aidA4	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: APH	F:	ECOD (20:10:01)
A		e4aidA6	A: POZ domain	X: POZ domain	H: POZ domain	T: PNPase	F:	ECOD (20:10:01)
B		e4aidB11	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: Peptidase_M49	F:	ECOD (20:10:01)
C		e4aidC1	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T: Aminotran_3	F:	ECOD (20:10:01)

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
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 endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity ribonuclease E activity hydrolase activity, acting on ester bonds cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity ribonuclease E activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity RNA binding rRNA binding nucleic acid binding transition metal ion binding zinc ion binding tRNA binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic 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 cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic 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 primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process ribonucleoprotein complex biogenesis rRNA processing nucleobase-containing compound biosynthetic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process tRNA metabolic process tRNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane side of membrane
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 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	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic 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 cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic 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 primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic 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
D [auth F], E [auth G], F [auth H]	IPR028878	Ribonuclease E	Family
D [auth F], E [auth G], F [auth H]	IPR004659	Ribonuclease E/G	Family
D [auth F], E [auth G], F [auth H]	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G	Domain
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
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

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.