8AFF

Wild type oxalyl-CoA synthetase Pcs60p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history


Literature

Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase.

Burgi, J.Lill, P.Giannopoulou, E.A.Jeffries, C.M.Chojnowski, G.Raunser, S.Gatsogiannis, C.Wilmanns, M.

(2023) Biol Chem 404: 195-207

  • DOI: https://doi.org/10.1515/hsz-2022-0273
  • Primary Citation of Related Structures:  
    8AFF, 8AFG, 8ATD

  • PubMed Abstract: 

    Oxalyl-CoA synthetase from Saccharomyces cerevisiae is one of the most abundant peroxisomal proteins in yeast and hence has become a model to study peroxisomal translocation. It contains a C-terminal Peroxisome Targeting Signal 1, which however is partly dispensable, suggesting additional receptor bindings sites. To unravel any additional features that may contribute to its capacity to be recognized as peroxisomal target, we determined its assembly and overall architecture by an integrated structural biology approach, including X-ray crystallography, single particle cryo-electron microscopy and small angle X-ray scattering. Surprisingly, it assembles into mixture of concentration-dependent dimers, tetramers and hexamers by dimer self-association. Hexameric particles form an unprecedented asymmetric horseshoe-like arrangement, which considerably differs from symmetric hexameric assembly found in many other protein structures. A single mutation within the self-association interface is sufficient to abolish any higher-level oligomerization, resulting in a homogenous dimeric assembly. The small C-terminal domain of yeast Oxalyl-CoA synthetase is connected by a partly flexible hinge with the large N-terminal domain, which provides the sole basis for oligomeric assembly. Our data provide a basis to mechanistically study peroxisomal translocation of this target.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxalate--CoA ligase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
543Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PCS60AAE3FAT2YBR222CYBR1512
EC: 6.2.1.8
UniProt
Find proteins for P38137 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38137 
Go to UniProtKB:  P38137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38137
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.029α = 90
b = 93.724β = 93.811
c = 356.488γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany1058/9-1
German Research Foundation (DFG)Germany1058/9-2
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermany664726

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description