8GR9

Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress.

Nishio, K.Kawarasaki, T.Sugiura, Y.Matsumoto, S.Konoshima, A.Takano, Y.Hayashi, M.Okumura, F.Kamura, T.Mizushima, T.Nakatsukasa, K.

(2023) Sci Adv 9: eadf1956-eadf1956

  • DOI: https://doi.org/10.1126/sciadv.adf1956
  • Primary Citation of Related Structures:  
    8GQZ, 8GR8, 8GR9, 8GRE, 8GRF

  • PubMed Abstract: 

    Deficiencies in mitochondrial protein import are associated with a number of diseases. However, although nonimported mitochondrial proteins are at great risk of aggregation, it remains largely unclear how their accumulation causes cell dysfunction. Here, we show that nonimported citrate synthase is targeted for proteasomal degradation by the ubiquitin ligase SCF Ucc1 . Unexpectedly, our structural and genetic analyses revealed that nonimported citrate synthase appears to form an enzymatically active conformation in the cytosol. Its excess accumulation caused ectopic citrate synthesis, which, in turn, led to an imbalance in carbon flux of sugar, a reduction of the pool of amino acids and nucleotides, and a growth defect. Under these conditions, translation repression is induced and acts as a protective mechanism that mitigates the growth defect. We propose that the consequence of mitochondrial import failure is not limited to proteotoxic insults, but that the accumulation of a nonimported metabolic enzyme elicits ectopic metabolic stress.


  • Organizational Affiliation

    Department of Life Science, Graduate School of Science, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase
A, B
460Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CIT2GI527_G0000583
EC: 2.3.3.16
UniProt
Find proteins for P08679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08679 
Go to UniProtKB:  P08679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08679
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
C [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
OAA (Subject of Investigation/LOI)
Query on OAA

Download Ideal Coordinates CCD File 
J [auth A]OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.079α = 90
b = 129.659β = 116.574
c = 68.127γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H03198
Japan Society for the Promotion of Science (JSPS)Japan24112009

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection