3GME

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.286 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.

Nurmohamed, S.Vaidialingam, B.Callaghan, A.J.Luisi, B.F.

(2009) J.Mol.Biol. 389: 17-33

  • DOI: 10.1016/j.jmb.2009.03.051
  • Primary Citation of Related Structures:  

  • PubMed 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 i ...

    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 beta-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.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyribonucleotide nucleotidyltransferase
A
549Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: pnp
EC: 2.7.7.8
Find proteins for A7ZS61 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZS61
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease E
D
41Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rne
EC: 3.1.26.12
Find proteins for A7ZKI9 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZKI9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.286 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 158.574α = 90.00
b = 158.574β = 90.00
c = 156.118γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance