Crystal structure of ras selenocysteine lyase in complex with selenopropionate

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase.

Omi, R.Kurokawa, S.Mihara, H.Hayashi, H.Goto, M.Miyahara, I.Kurihara, T.Hirotsu, K.Esaki, N.

(2010) J Biol Chem 285: 12133-12139

  • DOI: https://doi.org/10.1074/jbc.M109.084475
  • Primary Citation of Related Structures:  
    3A9X, 3A9Y, 3A9Z

  • PubMed Abstract: 

    Selenocysteine lyase (SCL) catalyzes the pyridoxal 5'-phosphate-dependent removal of selenium from l-selenocysteine to yield l-alanine. The enzyme is proposed to function in the recycling of the micronutrient selenium from degraded selenoproteins containing selenocysteine residue as an essential component. The enzyme exhibits strict substrate specificity toward l-selenocysteine and no activity to its cognate l-cysteine. However, it remains unclear how the enzyme distinguishes between selenocysteine and cysteine. Here, we present mechanistic studies of selenocysteine lyase from rat. ESI-MS analysis of wild-type and C375A mutant SCL revealed that the catalytic reaction proceeds via the formation of an enzyme-bound selenopersulfide intermediate on the catalytically essential Cys-375 residue. UV-visible spectrum analysis and the crystal structure of SCL complexed with l-cysteine demonstrated that the enzyme reversibly forms a nonproductive adduct with l-cysteine. Cys-375 on the flexible loop directed l-selenocysteine, but not l-cysteine, to the correct position and orientation in the active site to initiate the catalytic reaction. These findings provide, for the first time, the basis for understanding how trace amounts of a selenium-containing substrate is distinguished from excessive amounts of its cognate sulfur-containing compound in a biological system.

  • Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Selenocysteine lyase
A, B
432Rattus norvegicusMutation(s): 0 
Gene Names: Scly
Find proteins for Q68FT9 (Rattus norvegicus)
Explore Q68FT9 
Go to UniProtKB:  Q68FT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68FT9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.416α = 90
b = 101.206β = 90
c = 197.356γ = 90
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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references