3W1K

Crystal structure of the selenocysteine synthase SelA and tRNASec complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report



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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-seryl-tRNA(Sec) selenium transferaseABCDE452Aquifex aeolicus VF5Mutation(s): 4 
Gene Names: selAaq_1031
EC: 2.9.1.1
Find proteins for O67140 (Aquifex aeolicus (strain VF5))
Explore O67140 
Go to UniProtKB:  O67140
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
selenocysteine tRNAF, G, H, I, J95Caldanaerobacter subterraneus subsp. tengcongensis MB4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,B,C,D,EL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.553α = 90
b = 355.972β = 115.41
c = 165.495γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release