5SYN

Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).

Won, S.J.Davda, D.Labby, K.J.Hwang, S.Y.Pricer, R.Majmudar, J.D.Armacost, K.A.Rodriguez, L.A.Rodriguez, C.L.Chong, F.S.Torossian, K.A.Palakurthi, J.Hur, E.S.Meagher, J.L.Brooks, C.L.Stuckey, J.A.Martin, B.R.

(2016) ACS Chem Biol 11: 3374-3382

  • DOI: 10.1021/acschembio.6b00720
  • Primary Citation of Related Structures:  
    5SYN, 5SYM

  • PubMed Abstract: 
  • Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments ...

    Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments. This process is necessary for the trafficking and oncogenic signaling of S-palmitoylated Ras isoforms, and potentially many peripheral membrane proteins. The depalmitoylating enzymes APT1 and APT2 are separately conserved in all vertebrates, suggesting unique functional roles for each enzyme. The recent discovery of the APT isoform-selective inhibitors ML348 and ML349 has opened new possibilities to probe the function of each enzyme, yet it remains unclear how each inhibitor achieves orthogonal inhibition. Herein, we report the high-resolution structure of human APT2 in complex with ML349 (1.64 Å), as well as the complementary structure of human APT1 bound to ML348 (1.55 Å). Although the overall peptide backbone structures are nearly identical, each inhibitor adopts a distinct conformation within each active site. In APT1, the trifluoromethyl group of ML348 is positioned above the catalytic triad, but in APT2, the sulfonyl group of ML349 forms hydrogen bonds with active site resident waters to indirectly engage the catalytic triad and oxyanion hole. Reciprocal mutagenesis and activity profiling revealed several differing residues surrounding the active site that serve as critical gatekeepers for isoform accessibility and dynamics. Structural and biochemical analysis suggests the inhibitors occupy a putative acyl-binding region, establishing the mechanism for isoform-specific inhibition, hydrolysis of acyl substrates, and structural orthogonality important for future probe development.


    Organizational Affiliation

    Program in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences Institute, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-protein thioesterase 2A, B, C, D231Homo sapiensMutation(s): 0 
Gene Names: LYPLA2APT2
EC: 3.1.2
Find proteins for O95372 (Homo sapiens)
Explore O95372 
Go to UniProtKB:  O95372
NIH Common Fund Data Resources
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
71TKi:  200   nM  BindingDB
71TKi:  120   nM  BindingDB
71TKd:  240   nM  Binding MOAD
71TIC50:  1100   nM  BindingDB
71TKi:  660   nM  BindingDB
71TKi:  10000   nM  BindingDB
71TKd:  160   nM  BindingDB
71TKi:  230   nM  BindingDB
71TKd:  240   nM  BindingDB
71TIC50:  1000   nM  BindingDB
71TKi:  10000   nM  BindingDB
71TKi:  130   nM  BindingDB
71TKi:  10000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.21α = 90
b = 79.79β = 93.3
c = 138.61γ = 90
Software Package:
Software NamePurpose
Cootmodel building
BUSTERrefinement
SCALAdata scaling
BALBESphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR00 CA151460
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2 GM114848

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence