3H1C

Crystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.301 

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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:  
    3GCM, 3GLL, 3GME, 3H1C

  • 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 into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyribonucleotide nucleotidyltransferase549Escherichia coliMutation(s): 0 
EC: 2.7.7.8
UniProt
Find proteins for P05055 (Escherichia coli (strain K12))
Explore P05055 
Go to UniProtKB:  P05055
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05055
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease E41N/AMutation(s): 0 
EC: 3.1.26.12
UniProt
Find proteins for P21513 (Escherichia coli (strain K12))
Explore P21513 
Go to UniProtKB:  P21513
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21513
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO4
Query on WO4

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth C],
DA [auth G],
EA [auth I],
AA [auth B],
BA [auth B],
CA [auth C],
DA [auth G],
EA [auth I],
FA [auth K],
GA [auth K],
HA [auth M],
IA [auth M],
JA [auth O],
KA [auth O],
LA [auth R],
MA [auth R],
NA [auth T],
OA [auth T],
PA [auth V],
QA [auth V],
RA [auth X],
SA [auth X],
Y [auth A],
Z [auth A]
TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.57 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.301 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.742α = 90
b = 262.887β = 90
c = 264.125γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance