Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly
| Autor: | Bhamini Vaidialingam, Salima Nurmohamed, Ben F. Luisi, Anastasia J. Callaghan |
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| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: |
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Molecular polynucleotide phosphorylase RNase P Exosome complex RNase E Endoribonuclease Molecular Sequence Data protein-protein interactions Biology Calorimetry Crystallography X-Ray Article 03 medical and health sciences RNA degradation Structural Biology Multienzyme Complexes Exoribonuclease Catalytic Domain Endoribonucleases Escherichia coli Polynucleotide phosphorylase Amino Acid Sequence Protein Structure Quaternary Molecular Biology 030304 developmental biology Polyribonucleotide Nucleotidyltransferase 0303 health sciences Messenger RNA Manganese PNPase core PNPase ΔKHΔS1 lacking the C-terminal S1 and KH domains 030302 biochemistry & molecular biology RNA degradosome RNA Protein Structure Tertiary RNA Bacterial Biochemistry Biocatalysis PNPase polynucleotide phosphorylase (also known as polyribonucleotide nucleotidyltransferase) Degradosome RNA Helicases Protein Binding |
| Zdroj: | Journal of Molecular Biology |
| ISSN: | 1089-8638 0022-2836 |
| Popis: | Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. The homotrimeric PNPase engages RNase E on the periphery of its ring-like architecture through a pseudo-continuous anti-parallel β-sheet. A similar interaction pattern occurs in the structurally homologous human exosome between the Rrp45 and Rrp46 subunits. At the centre of the PNPase ring is a tapered channel with an adjustable aperture where RNA bases stack on phenylalanine side chains and trigger structural changes that propagate to the active sites. Manganese can substitute for magnesium as an essential co-factor for PNPase catalysis, and our crystal structure of the enzyme in complex with manganese suggests how the metal is positioned to stabilise the transition state. We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome. |
| Databáze: | OpenAIRE |
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