Crystal structure of mouse selenocysteine synthase

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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This is version 1.2 of the entry. See complete history


Structure and catalytic mechanism of eukaryotic selenocysteine synthase.

Ganichkin, O.M.Xu, X.M.Carlson, B.A.Mix, H.Hatfield, D.L.Gladyshev, V.N.Wahl, M.C.

(2008) J Biol Chem 283: 5849-5865

  • DOI: https://doi.org/10.1074/jbc.M709342200
  • Primary Citation of Related Structures:  
    3BC8, 3BCA, 3BCB

  • PubMed Abstract: 

    In eukaryotes and Archaea, selenocysteine synthase (SecS) converts O-phospho-L-seryl-tRNA [Ser]Sec into selenocysteyl-tRNA [Ser]Sec using selenophosphate as the selenium donor compound. The molecular mechanisms underlying SecS activity are presently unknown. We have delineated a 450-residue core of mouse SecS, which retained full selenocysteyl-tRNA [Ser]Sec synthesis activity, and determined its crystal structure at 1.65 A resolution. SecS exhibits three domains that place it in the fold type I family of pyridoxal phosphate (PLP)-dependent enzymes. Two SecS monomers interact intimately and together build up two identical active sites around PLP in a Schiff-base linkage with lysine 284. Two SecS dimers further associate to form a homotetramer. The N terminus, which mediates tetramer formation, and a large insertion that remodels the active site set SecS aside from other members of the family. The active site insertion contributes to PLP binding and positions a glutamate next to the PLP, where it could repel substrates with a free alpha-carboxyl group, suggesting why SecS does not act on free O-phospho-l-serine. Upon soaking crystals in phosphate buffer, a previously disordered loop within the active site insertion contracted to form a phosphate binding site. Residues that are strictly conserved in SecS orthologs but variant in related enzymes coordinate the phosphate and upon mutation corrupt SecS activity. Modeling suggested that the phosphate loop accommodates the gamma-phosphate moiety of O-phospho-l-seryl-tRNA [Ser]Sec and, after phosphate elimination, binds selenophosphate to initiate attack on the proposed aminoacrylyl-tRNA [Ser]Sec intermediate. Based on these results and on the activity profiles of mechanism-based inhibitors, we offer a detailed reaction mechanism for the enzyme.

  • Organizational Affiliation

    Max-Planck-Institut für Biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Am Fassberg 11, D-37077 Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-phosphoseryl-tRNA(Sec) selenium transferase450Mus musculusMutation(s): 0 
Gene Names: SepsecsD5Ertd135e
EC: 2.9.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P6M7 (Mus musculus)
Explore Q6P6M7 
Go to UniProtKB:  Q6P6M7
IMPC:  MGI:1098791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P6M7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.172α = 90
b = 138.73β = 90
c = 141.66γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description