Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 106.49 kDa 
• Atom Count: 6950 
• Residue Count: 860 
• Unique protein chains: 1

6GFL

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

• DOI: 10.2210/pdb6GFL/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-01 Released: 2019-04-24 
• Deposition Author(s): Zhang, Y., Baerentsen, R.L., Gerdes, K., Brodersen, D.E.
• Funding Organization(s): Danish National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.269 
• R-Value Work: 0.212 

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

• PubMed: 31023582 
• DOI: 10.1016/j.molcel.2019.03.035
• Primary Citation of Related Structures:  
  6GFM, 6GFL


• 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.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Centre of Excellence for Bacterial Stress Response and Persistence (BASP), Aarhus University, 8000 Aarhus C, Denmark. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	A, B	474	Escherichia coli K-12	Mutation(s): 0  Gene Names: ppnN, ygdH, b2795, JW2766 EC: 3.2.2 (PDB Primary Data), 3.2.2.10 (PDB Primary Data), 3.2.2.4 (PDB Primary Data)
Find proteins for P0ADR8 (Escherichia coli (strain K12)) Explore P0ADR8  Go to UniProtKB:  P0ADR8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 94.17	α = 90
b = 101.08	β = 90
c = 112.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-01 
• Released Date: 2019-04-24 
Deposition Author(s): Zhang, Y., Baerentsen, R.L., Gerdes, K., Brodersen, D.E.

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Funding Organization	Location	Grant Number
Danish National Research Foundation	Denmark	DNRF120

Revision History 

• 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