3W1J | pdb_00003w1j

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.266 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 441.97 kDa 
  • Atom Count: 30,888 
  • Modeled Residue Count: 3,913 
  • Deposited Residue Count: 3,920 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-seryl-tRNA(Sec) selenium transferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
392Aquifex aeolicus VF5Mutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THJ

Query on THJ


Download:Ideal Coordinates CCD File
AA [auth I]
BA [auth I]
CA [auth J]
DA [auth J]
EA [auth J]
AA [auth I],
BA [auth I],
CA [auth J],
DA [auth J],
EA [auth J],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth C],
R [auth D],
S [auth D],
U [auth E],
V [auth E],
W [auth E],
Y [auth H]
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
K

Query on K


Download:Ideal Coordinates CCD File
K [auth A],
Q [auth D],
T [auth E],
X [auth G],
Z [auth I]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E
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: 3.25 Å
  • R-Value Free:  0.266 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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
DENZOdata reduction
SCALEPACKdata scaling
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: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection