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 

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Ligand Structure Quality Assessment 


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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: https://doi.org/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). 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Selenide, water dikinase 1
A, B
394Homo sapiensMutation(s): 0 
Gene Names: SEPHS1SELDSPSSPS1
EC: 2.7.9.3
UniProt & NIH Common Fund Data Resources
Find proteins for P49903 (Homo sapiens)
Explore P49903 
Go to UniProtKB:  P49903
PHAROS:  P49903
GTEx:  ENSG00000086475 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49903
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations