3FD5

Crystal structure of human selenophosphate synthetase 1 complex with AMPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 1A, B394Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP2
Query on AP2

Download Ideal Coordinates CCD File 
C [auth A], I [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H17 N5 O9 P2
OLCWZBFDIYXLAA-IOSLPCCCSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A], J [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
H [auth A], M [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], N [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.734α = 90
b = 66.734β = 90
c = 181.168γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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