NDLI: Crystal Structure of Escherichia coli Polynucleotide Phosphorylase Core Bound to RNase E, RNA and Manganese: Implications for Catalytic Mechanism and RNA Degradosome Assembly

Content Provider	PubMed Central
Author	Salima, Nurmohamed Vaidialingam, Bhamini Callaghan, Anastasia J. Luisi, Ben F.
Copyright Year	2009
Abstract	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.
Related Links	http://dx.doi.org/10.1016/j.jmb.2009.03.051
Ending Page	33
Page Count	17
Starting Page	17
File Format	PDF
ISSN	00222836
e-ISSN	10898638
Journal	Journal of Molecular Biology
Issue Number	1-3
Volume Number	389
Language	English
Publisher	Elsevier
Publisher Date	2009-05-01
Access Restriction	Open
Rights Holder	Elsevier
Subject Keyword	Molecular Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Structural Biology Molecular Biology Biophysics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly

The Crystal Structure of the Escherichia coli RNase E Apoprotein and a Mechanism for RNA Degradation

A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability

The proteomic response to mutants of the Escherichia coli RNA degradosome

Escherichia coli Poly(A)-binding Proteins That Interact with Components of Degradosomes or Impede RNA Decay Mediated by Polynucleotide Phosphorylase and RNase E

A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability

The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome

Regulation of mRNA Decay in Bacteria

RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression

Crystal Structure of Escherichia coli Polynucleotide Phosphorylase Core Bound to RNase E, RNA and Manganese: Implications for Catalytic Mechanism and RNA Degradosome Assembly

Similar Documents

Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly

The Crystal Structure of the Escherichia coli RNase E Apoprotein and a Mechanism for RNA Degradation

A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability

The proteomic response to mutants of the Escherichia coli RNA degradosome

Escherichia coli Poly(A)-binding Proteins That Interact with Components of Degradosomes or Impede RNA Decay Mediated by Polynucleotide Phosphorylase and RNase E

A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability

The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome

Regulation of mRNA Decay in Bacteria

RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression

Crystal Structure of Escherichia coli Polynucleotide Phosphorylase Core Bound to RNase E, RNA and Manganese: Implications for Catalytic Mechanism and RNA Degradosome Assembly