3FD6

Crystal structure of human selenophosphate synthetase 1 complex with ADP and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structures of catalytic intermediates of human selenophosphate synthetase 1.

Wang, K.T.Wang, J.Li, L.F.Su, X.D.

(2009) J Mol Biol 390: 747-759

  • DOI: 10.1016/j.jmb.2009.05.032
  • Primary Citation of Related Structures:  
    3FD5, 3FD6

  • PubMed Abstract: 
  • Selenophosphate synthetase catalyzes the synthesis of the highly active selenium donor molecule selenophosphate, a key intermediate in selenium metabolism. We have determined the high-resolution crystal structure of human selenophosphate synthetase 1 (hSPS1) ...

    Selenophosphate synthetase catalyzes the synthesis of the highly active selenium donor molecule selenophosphate, a key intermediate in selenium metabolism. We have determined the high-resolution crystal structure of human selenophosphate synthetase 1 (hSPS1). An unexpected reaction intermediate, with a tightly bound phosphate and ADP at the active site has been captured in the structure. An enzymatic assay revealed that hSPS1 possesses low ADP hydrolysis activity in the presence of phosphate. Our structural and enzymatic results suggest that consuming the second high-energy phosphoester bond of ATP could protect the labile product selenophosphate during catalytic reaction. We solved another hSPS1 structure with potassium ions at the active sites. Comparing the two structures, we were able to define the monovalent cation-binding site of the enzyme. The detailed mechanism of the ADP hydrolysis step and the exact function of the monovalent cation for hSPS1 catalytic reaction are proposed.


    Organizational Affiliation

    National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, P.R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Selenide, water dikinase 1 AB394Homo sapiensMutation(s): 0 
Gene Names: SEPHS1SELDSPSSPS1
EC: 2.7.9.3
Find proteins for P49903 (Homo sapiens)
Explore P49903 
Go to UniProtKB:  P49903
NIH Common Fund Data Resources
PHAROS:  P49903
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.618α = 90
b = 67.618β = 90
c = 182.551γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHENIXmodel building
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-11-25 
  • Released Date: 2009-09-22 
  • Deposition Author(s): Wang, K.T.

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance