6ECB

Vlm2 thioesterase domain wild type structure 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.

Huguenin-Dezot, N.Alonzo, D.A.Heberlig, G.W.Mahesh, M.Nguyen, D.P.Dornan, M.H.Boddy, C.N.Schmeing, T.M.Chin, J.W.

(2019) Nature 565: 112-117

  • DOI: 10.1038/s41586-018-0781-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many enzymes catalyse reactions that proceed through covalent acyl-enzyme (ester or thioester) intermediates 1 . These enzymes include serine hydrolases 2,3 (encoded by one per cent of human genes, and including serine protease ...

    Many enzymes catalyse reactions that proceed through covalent acyl-enzyme (ester or thioester) intermediates 1 . These enzymes include serine hydrolases 2,3 (encoded by one per cent of human genes, and including serine proteases and thioesterases), cysteine proteases (including caspases), and many components of the ubiquitination machinery 4,5 . Their important acyl-enzyme intermediates are unstable, commonly having half-lives of minutes to hours 6 . In some cases, acyl-enzyme complexes can be stabilized using substrate analogues or active-site mutations but, although these approaches can provide valuable insight 7-10 , they often result in complexes that are substantially non-native. Here we develop a strategy for incorporating 2,3-diaminopropionic acid (DAP) into recombinant proteins, via expansion of the genetic code 11 . We show that replacing catalytic cysteine or serine residues of enzymes with DAP permits their first-step reaction with native substrates, allowing the efficient capture of acyl-enzyme complexes that are linked through a stable amide bond. For one of these enzymes, the thioesterase domain of valinomycin synthetase 12 , we elucidate the biosynthetic pathway by which it progressively oligomerizes tetradepsipeptidyl substrates to a dodecadepsipeptidyl intermediate, which it then cyclizes to produce valinomycin. By trapping the first and last acyl-thioesterase intermediates in the catalytic cycle as DAP conjugates, we provide structural insight into how conformational changes in thioesterase domains of such nonribosomal peptide synthetases control the oligomerization and cyclization of linear substrates. The encoding of DAP will facilitate the characterization of diverse acyl-enzyme complexes, and may be extended to capturing the native substrates of transiently acylated proteins of unknown function.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. chin@mrc-lmb.cam.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vlm2
A
303Streptomyces tsusimaensisMutation(s): 0 
Gene Names: vlm2
EC: 3.1.2
Find proteins for Q1PSF3 (Streptomyces tsusimaensis)
Go to UniProtKB:  Q1PSF3
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.399α = 90
b = 151.399β = 90
c = 151.399γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada106615

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence