2ZAU

Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

Matsumoto, E., Sekine, S., Akasaka, R., Otta, Y., Katsura, K., Inoue, M., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 453-458

  • DOI: 10.1107/S1744309108012074
  • Primary Citation of Related Structures:  
    2ZAU

  • PubMed Abstract: 

    • Selenophosphate synthetase (SPS) catalyzes the activation of selenide with ATP to synthesize selenophosphate, the reactive selenium donor for biosyntheses of both the 21st amino acid selenocysteine and 2-selenouridine nucleotides in tRNA anticodons. The crystal structure of an N-terminally (25 residues) truncated fragment of SPS (SPS-DeltaN) from Aquifex aeolicus has been determined at 2 ...

    Selenophosphate synthetase (SPS) catalyzes the activation of selenide with ATP to synthesize selenophosphate, the reactive selenium donor for biosyntheses of both the 21st amino acid selenocysteine and 2-selenouridine nucleotides in tRNA anticodons. The crystal structure of an N-terminally (25 residues) truncated fragment of SPS (SPS-DeltaN) from Aquifex aeolicus has been determined at 2.0 A resolution. The structure revealed SPS to be a two-domain alpha/beta protein, with domain folds that are homologous to those of PurM-superfamily proteins. In the crystal, six monomers of SPS-DeltaN form a hexamer of 204 kDa, whereas the molecular weight estimated by ultracentrifugation was approximately 63 kDa, which is comparable to the calculated weight of the dimer (68 kDa).

    Organizational Affiliation: 

    Systems and Structural Biology Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Selenide, water dikinaseA, B, C311Aquifex aeolicusMutation(s): 0 
Gene Names: selD
EC: 2.7.9.3
UniProt
Find proteins for O67139 (Aquifex aeolicus (strain VF5))
Explore O67139 
Go to UniProtKB:  O67139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67139
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.161α = 90
b = 165.198β = 90
c = 167.684γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance