4DQJ

Structural Investigation of Bacteriophage Phi6 Lysin (in complex with chitotetraose)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzyme.

Dessau, M.Goldhill, D.McBride, R.McBride, R.L.Turner, P.E.Modis, Y.

(2012) PLoS Genet 8: e1003102-e1003102

  • DOI: 10.1371/journal.pgen.1003102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection. The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments th ...

    The modulation of fitness by single mutational substitutions during environmental change is the most fundamental consequence of natural selection. The antagonistic tradeoffs of pleiotropic mutations that can be selected under changing environments therefore lie at the foundation of evolutionary biology. However, the molecular basis of fitness tradeoffs is rarely determined in terms of how these pleiotropic mutations affect protein structure. Here we use an interdisciplinary approach to study how antagonistic pleiotropy and protein function dictate a fitness tradeoff. We challenged populations of an RNA virus, bacteriophage Φ6, to evolve in a novel temperature environment where heat shock imposed extreme virus mortality. A single amino acid substitution in the viral lysin protein P5 (V207F) favored improved stability, and hence survival of challenged viruses, despite a concomitant tradeoff that decreased viral reproduction. This mutation increased the thermostability of P5. Crystal structures of wild-type, mutant, and ligand-bound P5 reveal the molecular basis of this thermostabilization--the Phe207 side chain fills a hydrophobic cavity that is unoccupied in the wild-type--and identify P5 as a lytic transglycosylase. The mutation did not reduce the enzymatic activity of P5, suggesting that the reproduction tradeoff stems from other factors such as inefficient capsid assembly or disassembly. Our study demonstrates how combining experimental evolution, biochemistry, and structural biology can identify the mechanisms that drive the antagonistic pleiotropic phenotypes of an individual point mutation in the classic evolutionary tug-of-war between survival and reproduction.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane protein Phi6 P5
A, B
173Pseudomonas phage phi6Mutations: F160V
Gene Names: p5a (P5a)
Find proteins for Q283U5 (Pseudomonas phage phi6)
Go to UniProtKB:  Q283U5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AES
Query on AES

Download SDF File 
Download CCD File 
A
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
AEBSF
C8 H10 F N O2 S
MGSKVZWGBWPBTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.816α = 90.00
b = 50.936β = 103.48
c = 65.020γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references