4AIM

Crystal structure of C. crescentus PNPase bound to RNase E recognition peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly.

Hardwick, S.W.Gubbey, T.Hug, I.Jenal, U.Luisi, B.F.

(2012) Open Biol. 2: 20028

  • DOI: 10.1098/rsob.120028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sit ...

    Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
A
726Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Gene Names: pnp
EC: 2.7.7.8
Find proteins for Q9AC32 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9AC32
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
C
14Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Gene Names: rne
EC: 3.1.26.12
Find proteins for Q9A749 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A749
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 97.329α = 90.00
b = 97.329β = 90.00
c = 191.910γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Other
  • Version 1.2: 2014-02-05
    Type: Database references, Source and taxonomy