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

Experimental Data Snapshot

  • Resolution: 1.23 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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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: https://doi.org/10.1371/journal.pgen.1003102
  • Primary Citation of Related Structures:  
    4DQ5, 4DQ7, 4DQJ

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein Phi6 P5
A, B
173Cystovirus phi6Mutation(s): 1 
Gene Names: P5p5a
Find proteins for Q283U5 (Cystovirus phi6)
Explore Q283U5 
Go to UniProtKB:  Q283U5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ283U5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AES

Download Ideal Coordinates CCD File 
C8 H10 F N O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.23 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.816α = 90
b = 50.936β = 103.48
c = 65.02γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary