8GQZ | pdb_00008gqz

Crystal structure of mitochondrial citrate synthase (Cit1) from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.197 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GQZ

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 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.

Macromolecule Content 

  • Total Structure Weight: 107.24 kDa 
  • Atom Count: 8,025 
  • Modeled Residue Count: 877 
  • Deposited Residue Count: 958 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Citrate synthase
A, B
479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CIT1GI527_G0005109
EC: 2.3.3.1
UniProt
Find proteins for P00890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00890 
Go to UniProtKB:  P00890
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00890
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.197 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.328α = 90
b = 102.398β = 90
c = 146.87γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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