X-ray structure of wild-type E. coli Acyl-CoA thioesterase I at pH 5

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1021/acscatal.7b00408
  • Primary Citation of Related Structures:  
    5TIC, 5TID, 5TIE, 5TIF

  • 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 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 Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA thioesterase I
A, B
185Escherichia coliMutation(s): 0 
Gene Names: tesAapeApldCb0494JW0483
EC: 3.1.2 (PDB Primary Data), (PDB Primary Data)
Find proteins for P0ADA1 (Escherichia coli (strain K12))
Explore P0ADA1 
Go to UniProtKB:  P0ADA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADA1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.922α = 90
b = 82.124β = 90.44
c = 53.903γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115921

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description