7OBM

Crystal structure of the human Prolyl Endopeptidase-Like protein short form (residues 90-727)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function.

Rosier, K.McDevitt, M.T.Smet, J.Floyd, B.J.Verschoore, M.Marcaida, M.J.Bingman, C.A.Lemmens, I.Dal Peraro, M.Tavernier, J.Cravatt, B.F.Gounko, N.V.Vints, K.Monnens, Y.Bhalla, K.Aerts, L.Rashan, E.H.Vanlander, A.V.Van Coster, R.Regal, L.Pagliarini, D.J.Creemers, J.W.M.

(2021) iScience 24: 103460-103460

  • DOI: https://doi.org/10.1016/j.isci.2021.103460
  • Primary Citation of Related Structures:  
    7OBM

  • PubMed Abstract: 

    Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPL L isoform localizes to mitochondria, whereas PREPL S remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPL L is involved in mitochondrial homeostasis.


  • Organizational Affiliation

    Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl endopeptidase-like639Homo sapiensMutation(s): 0 
Gene Names: PREPLKIAA0436
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q4J6C6 (Homo sapiens)
Explore Q4J6C6 
Go to UniProtKB:  Q4J6C6
PHAROS:  Q4J6C6
GTEx:  ENSG00000138078 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4J6C6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.92α = 90
b = 150.88β = 90
c = 220.66γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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 StatesU54 GM074901
Research Foundation - Flanders (FWO)BelgiumG0B9119N
KU LeuvenBelgiumC14/16/070

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references