5AC8

S. enterica HisA with mutations D10G, dup13-15, G102A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.699 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes.

Newton, M.S.Guo, X.Soderholm, A.Nasvall, J.Lundstrom, P.Andersson, D.I.Selmer, M.Patrick, W.M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4727-4732

  • DOI: 10.1073/pnas.1618552114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dyna ...

    New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (βα)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (βα)8 barrel as an inherently evolvable protein scaffold.


    Organizational Affiliation

    Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N/A
A
256Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 2 
Gene Names: hisA
EC: 5.3.1.16
Find proteins for P10372 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P10372
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.699 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.196 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.415α = 90.00
b = 86.415β = 90.00
c = 122.027γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-05-10
    Type: Database references