C-DES Mutant K223A with GLY Covalenty Linked to the PLP-cofactor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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This is version 1.4 of the entry. See complete history


Snapshots of the Cystine Lyase "C-DES" during Catalysis: Studies in Solution and in the Crystalline State

Kaiser, J.T.Bruno, S.Clausen, T.Huber, R.Schiaretti, F.Mozzarelli, A.Kessler, D.

(2003) J Biol Chem 278: 357-365

  • DOI: https://doi.org/10.1074/jbc.M209862200
  • Primary Citation of Related Structures:  
    1N2T, 1N31

  • PubMed Abstract: 

    The cystine lyase (C-DES) of Synechocystis is a pyridoxal-5'-phosphate-dependent enzyme distantly related to the family of NifS-like proteins. The crystal structure of an N-terminal modified variant has recently been determined. Herein, the reactivity of this enzyme variant was investigated spectroscopically in solution and in the crystalline state to follow the course of the reaction and to determine the catalytic mechanism on a molecular level. Using the stopped-flow technique, the reaction with the preferred substrate cystine was found to follow biphasic kinetics leading to the formation of absorbing species at 338 and 470 nm, attributed to the external aldimine and the alpha-aminoacrylate; the reaction with cysteine also exhibited biphasic behavior but only the external aldimine accumulated. The same reaction intermediates were formed in crystals as seen by polarized absorption microspectrophotometry, thus indicating that C-DES is catalytically competent in the crystalline state. The three-dimensional structure of the catalytically inactive mutant C-DES(K223A) in the presence of cystine showed the formation of an external aldimine species, in which two alternate conformations of the substrate were observed. The combined results allow a catalytic mechanism to be proposed involving interactions between cystine and the active site residues Arg-360, Arg-369, and Trp-251*; these residues reorient during the beta-elimination reaction, leading to the formation of a hydrophobic pocket that stabilizes the enolimine tautomer of the aminoacrylate and the cysteine persulfide product.

  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, Martinsried 82152, Germany. kaiser@biochem.mpg.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-cysteine/cystine lyase C-DES
A, B
386Synechocystis sp. PCC 6714Mutation(s): 1 
Gene Names: C-DES
EC: 4.4.1
Find proteins for Q9ZHG9 (Synechocystis sp. (strain PCC 6714))
Explore Q9ZHG9 
Go to UniProtKB:  Q9ZHG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZHG9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.752α = 90
b = 66.237β = 90
c = 172.792γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection, Refinement description