3W1H

Crystal structure of the selenocysteine synthase SelA from Aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation

Itoh, Y.Brocker, M.J.Sekine, S.Hammond, G.Suetsugu, S.Soll, D.Yokoyama, S.

(2013) Science 340: 75-78

  • DOI: https://doi.org/10.1126/science.1229521
  • Primary Citation of Related Structures:  
    3W1H, 3W1I, 3W1J, 3W1K

  • PubMed Abstract: 

    The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms Sec from phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus SelA complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four SelA subunits. The SelA N-terminal domain binds the tRNA(Sec)-specific D-arm structure, thereby discriminating Ser-tRNA(Sec) from Ser-tRNA(Ser). A large cleft is created between two subunits and accommodates the 3'-terminal region of Ser-tRNA(Sec). The SelA structures together with in vivo and in vitro enzyme assays show decamerization to be essential for SelA function. SelA catalyzes pyridoxal 5'-phosphate-dependent Sec formation involving Arg residues nonhomologous to those in SepSecS. Different protein architecture and substrate coordination of the bacterial enzyme provide structural evidence for independent evolution of the two Sec synthesis systems present in nature.


  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-seryl-tRNA(Sec) selenium transferase
A, B, C, D, E
452Aquifex aeolicus VF5Mutation(s): 4 
Gene Names: selA
EC: 2.9.1.1
UniProt
Find proteins for O67140 (Aquifex aeolicus (strain VF5))
Explore O67140 
Go to UniProtKB:  O67140
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67140
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.033α = 90
b = 167.033β = 90
c = 211.109γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-12-06
    Changes: Data collection