3W1J

Crystal structure of the N-terminal truncated selenocysteine synthase SelA in complex with thiosulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.252 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.1229521
  • Primary Citation of Related Structures:  3W1H, 3W1I, 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-seryl-tRNA(Sec) selenium transferase
A, B, C, D, E, F, G, H, I, J
392Aquifex aeolicus (strain VF5)Gene Names: selA
EC: 2.9.1.1
Find proteins for O67140 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67140
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, D, E, G, I
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
THJ
Query on THJ

Download SDF File 
Download CCD File 
A, B, C, D, E, H, I, J
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.252 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 92.442α = 102.09
b = 116.372β = 93.39
c = 124.788γ = 106.06
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
ADSCdata collection
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description