6GFM

Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 2.3 of the entry. See complete history

Literature

(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: 10.1016/j.molcel.2019.03.035
  • Primary Citation of Related Structures:  

  • 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 monophosph ...

    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.,Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark. Electronic address: deb@mbg.au.dk.,Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark.,Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
A
474Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ppnN (ygdH)
EC: 3.2.2.-, 3.2.2.10
Find proteins for P0ADR8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADR8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0O2
Query on 0O2

Download SDF File 
Download CCD File 
A
guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
C10 H18 N5 O20 P5
KCPMACXZAITQAX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 176.920α = 90.00
b = 176.920β = 90.00
c = 94.480γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF120

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 2.0: 2019-05-01
    Type: Atomic model, Data collection, Database references
  • Version 2.1: 2019-05-08
    Type: Data collection, Database references
  • Version 2.2: 2019-07-03
    Type: Data collection, Database references
  • Version 2.3: 2019-07-31
    Type: Data collection, Database references