Crystal structure of the Escherichia coli nucleosidase PpnN (apo form)

Experimental Data Snapshot

  • Resolution: 2.48 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 

Starting Model: experimental
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(p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.

Zhang, Y.E.Baerentsen, R.L.Fuhrer, T.Sauer, U.Gerdes, K.Brodersen, D.E.

(2019) Mol Cell 74: 1239

  • DOI: https://doi.org/10.1016/j.molcel.2019.03.035
  • Primary Citation of Related Structures:  
    6GFL, 6GFM

  • PubMed Abstract: 

    The stringent response alarmones pppGpp and ppGpp are essential for rapid adaption of bacterial physiology to changes in the environment. In Escherichia coli, the nucleosidase PpnN (YgdH) regulates purine homeostasis by cleaving nucleoside monophosphates and specifically binds (p)ppGpp. Here, we show that (p)ppGpp stimulates the catalytic activity of PpnN both in vitro and in vivo causing accumulation of several types of nucleobases during stress. The structure of PpnN reveals a tetramer with allosteric (p)ppGpp binding sites located between subunits. pppGpp binding triggers a large conformational change that shifts the two terminal domains to expose the active site, providing a structural rationale for the stimulatory effect. We find that PpnN increases fitness and adjusts cellular tolerance to antibiotics and propose a model in which nucleotide levels can rapidly be adjusted during stress by simultaneous inhibition of biosynthesis and stimulation of degradation, thus achieving a balanced physiological response to constantly changing environments.

  • Organizational Affiliation

    Department of Biology, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, 2200 Copenhagen, Denmark. Electronic address: yong.zhang@bio.ku.dk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
A, B
474Escherichia coli K-12Mutation(s): 0 
Gene Names: ppnNygdHb2795JW2766
EC: 3.2.2 (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for P0ADR8 (Escherichia coli (strain K12))
Explore P0ADR8 
Go to UniProtKB:  P0ADR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADR8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.48 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.17α = 90
b = 101.08β = 90
c = 112.29γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF120

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.4: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Refinement description