6K5V

Structure of CSY4 Apo-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical characterization of mitochondrial citrate synthase 4 from Arabidopsis thaliana.

Nishio, K.Mizushima, T.

(2020) Acta Crystallogr F Struct Biol Commun 76: 109-115

  • DOI: https://doi.org/10.1107/S2053230X20001521
  • Primary Citation of Related Structures:  
    6K5V

  • PubMed Abstract: 

    Citrate synthase (CS) catalyzes the conversion of oxaloacetate and acetyl coenzyme A into citrate and coenzyme A in the mitochondrial tricarboxylic acid (TCA) cycle. In plants, mitochondrial metabolism, including the TCA cycle, occurs in interaction with photosynthetic metabolism. The controlled regulation of several enzymes in the TCA cycle, such as CS, is important in plants. Here, the first crystal structure of a plant mitochondrial CS, CSY4 from Arabidopsis thaliana (AtCSY4), has been determined. Structural comparison of AtCSY4 with mitochondrial CSs revealed a high level of similarity. Inhibition analysis showed a similar manner of inhibition as in mitochondrial CSs. The effect of oxidation on one of a pair of cysteine residues in AtCSY4 was speculated upon based on the folded structure.


  • Organizational Affiliation

    Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase 4, mitochondrial
A, B, C, D, E
A, B, C, D, E, F
458Arabidopsis thalianaMutation(s): 0 
Gene Names: CSY4At2g44350F4I1.16
EC: 2.3.3.16
UniProt
Find proteins for P20115 (Arabidopsis thaliana)
Explore P20115 
Go to UniProtKB:  P20115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20115
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.35α = 90
b = 67.938β = 100.859
c = 317.823γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description