5TIF

x-ray structure of acyl-CoA thioesterase I, TesA, triple mutant M141L/Y145K/L146K in complex with octanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.

Grisewood, M.J.Hernandez Lozada, N.J.Thoden, J.B.Gifford, N.P.Mendez-Perez, D.Schoenberger, H.A.Allan, M.F.Floy, M.E.Lai, R.Y.Holden, H.M.Pfleger, B.F.Maranas, C.D.

(2017) ACS Catal 7: 3837-3849

  • DOI: 10.1021/acscatal.7b00408
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to acc ...

    Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e. binding selectivity). Here, we demonstrate this approach by identifying medium-chain (C 6 -C 12 ) acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, products of thioesterase-catalyzed hydrolysis, are limited in natural abundance compared to long-chain fatty acids; the limited supply leads to high costs of C 6 -C 10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding to the highly-active 'TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C 12 - or C 8 -specificity while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified three thioesterases with enhanced production of dodecanoic acid (C 12 ) and twenty-seven thioesterases with enhanced production of octanoic acid (C 8 ). The top variants reached up to 49% C 12 and 50% C 8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of 'TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of 'TesA variants suggest that hydrophobic forces govern 'TesA substrate specificity. We expect that the design rules we uncovered and the thioesterase variants identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain oleochemicals.


    Organizational Affiliation

    Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-CoA thioesterase I
A
185Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: tesA (apeA, pldC)
Find proteins for P0ADA1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADA1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
OCA
Query on OCA

Download SDF File 
Download CCD File 
A
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.500α = 90.00
b = 55.000β = 104.90
c = 42.000γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
REFMACrefinement
SAINTdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115921

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2018-02-14
    Type: Database references