6NY9

Alpha/beta hydrolase domain-containing protein 10 from mouse


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5.

Cao, Y.Qiu, T.Kathayat, R.S.Azizi, S.A.Thorne, A.K.Ahn, D.Fukata, Y.Fukata, M.Rice, P.A.Dickinson, B.C.

(2019) Nat Chem Biol 15: 1232-1240

  • DOI: https://doi.org/10.1038/s41589-019-0399-y
  • Primary Citation of Related Structures:  
    6NY9

  • PubMed Abstract: 

    S-Palmitoylation is a reversible lipid post-translational modification that has been observed on mitochondrial proteins, but both the regulation and functional consequences of mitochondrial S-palmitoylation are poorly understood. Here, we show that perturbing the 'erasers' of S-palmitoylation, acyl protein thioesterases (APTs), with either pan-active inhibitors or a mitochondrial-targeted APT inhibitor, diminishes the antioxidant buffering capacity of mitochondria. Surprisingly, this effect was not mediated by the only known mitochondrial APT, but rather by a resident mitochondrial protein with no known endogenous function, ABHD10. We show that ABHD10 is a member of the APT family of regulatory proteins and identify peroxiredoxin-5 (PRDX5), a key antioxidant protein, as a target of ABHD10 S-depalmitoylase activity. We then find that ABHD10 regulates the S-palmitoylation status of the nucleophilic active site residue of PRDX5, providing a direct mechanistic connection between ABHD10-mediated S-depalmitoylation of PRDX5 and its antioxidant capacity.


  • Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mycophenolic acid acyl-glucuronide esterase, mitochondrialA [auth B]250Mus musculusMutation(s): 0 
Gene Names: Abhd10
EC: 3.1.1.93
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PE15 (Mus musculus)
Explore Q6PE15 
Go to UniProtKB:  Q6PE15
IMPC:  MGI:2442422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PE15
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.388α = 90
b = 99.388β = 90
c = 149.597γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM119840

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description