6LHM

Structure of human PYCR2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.332 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.

Escande-Beillard, N.Loh, A.Saleem, S.N.Kanata, K.Hashimoto, Y.Altunoglu, U.Metoska, A.Grandjean, J.Ng, F.M.Pomp, O.Baburajendran, N.Wong, J.Hill, J.Beillard, E.Cozzone, P.Zaki, M.Kayserili, H.Hamada, H.Shiratori, H.Reversade, B.

(2020) Neuron 107: 82-94.e6

  • DOI: https://doi.org/10.1016/j.neuron.2020.03.028
  • Primary Citation of Related Structures:  
    6LHM

  • PubMed Abstract: 

    Patients lacking PYCR2, a mitochondrial enzyme that synthesizes proline, display postnatal degenerative microcephaly with hypomyelination. Here we report the crystal structure of the PYCR2 apo-enzyme and show that a novel germline p.Gly249Val mutation lies at the dimer interface and lowers its enzymatic activity. We find that knocking out Pycr2 in mice phenocopies the human disorder and depletes PYCR1 levels in neural lineages. In situ quantification of neurotransmitters in the brains of PYCR2 mutant mice and patients revealed a signature of encephalopathy driven by excessive cerebral glycine. Mechanistically, we demonstrate that loss of PYCR2 upregulates SHMT2, which is responsible for glycine synthesis. This hyperglycemia could be partially reversed by SHMT2 knockdown, which rescued the axonal beading and neurite lengths of cultured Pycr2 knockout neurons. Our findings identify the glycine metabolic pathway as a possible intervention point to alleviate the neurological symptoms of PYCR2-mutant patients.


  • Organizational Affiliation

    Institute of Medical Biology, Human Genetics and Embryology Laboratory, A(∗)STAR, Singapore 138648, Singapore; Genome Institute of Singapore, A∗STAR, Singapore 138672, Singapore; Department of Medical Genetics, Koç University, School of Medicine, 34010 Istanbul, Turkey. Electronic address: nathalie.escande@reversade.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroline-5-carboxylate reductase 2
A, B, C, D, E
301Homo sapiensMutation(s): 0 
Gene Names: PYCR2
EC: 1.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C36 (Homo sapiens)
Explore Q96C36 
Go to UniProtKB:  Q96C36
PHAROS:  Q96C36
GTEx:  ENSG00000143811 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96C36
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.332 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.903α = 90
b = 110.312β = 90
c = 155.465γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description