1X6V

The crystal structure of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Crystal Structure of Human PAPS Synthetase 1 Reveals Asymmetry in Substrate Binding

Harjes, S.Bayer, P.Scheidig, A.J.

(2005) J.Mol.Biol. 347: 623-635

  • DOI: 10.1016/j.jmb.2005.01.005
  • Primary Citation of Related Structures:  1XJQ, 1XNJ

  • PubMed Abstract: 
  • The high energy sulfate donor 3'-phosphoadenosine-5-phosphosulfate (PAPS) is used for sulfate conjugation of extracellular matrix, hormones and drugs. Human PAPS synthetase 1 catalyzes two subsequent reactions starting from ATP and sulfate. First the ...

    The high energy sulfate donor 3'-phosphoadenosine-5-phosphosulfate (PAPS) is used for sulfate conjugation of extracellular matrix, hormones and drugs. Human PAPS synthetase 1 catalyzes two subsequent reactions starting from ATP and sulfate. First the ATP sulfurylase domain forms APS, then the APS kinase domain phosphorylates the APS intermediate to PAPS. Up to now the interaction between the two enzymatic activities remained elusive, mainly because of missing structural information. Here we present the crystal structure of human PAPSS1 at 1.8 angstroms resolution. The structure reveals a homodimeric, asymmetric complex with the shape of a chair. The two kinase domains adopt different conformational states, with only one being able to bind its two substrates. The asymmetric binding of ADP to the APS kinase is not only observed in the crystal structure, but can also be detected in solution, using an enzymatic assay. These observations strongly indicate structural changes during the reaction cycle. Furthermore crystals soaked with ADP and APS could be prepared and the corresponding structures could be solved.


    Organizational Affiliation

    Molekulare und Strukturelle Biophysik, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, and Interdisciplinary Center of Magnetic Resonance (IZMR), 44227 Dortmund, Germany. stefan.harjes@gmx.net




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
B, A
630Homo sapiensGene Names: PAPSS1 (ATPSK1, PAPSS)
EC: 2.7.7.4, 2.7.1.25
Find proteins for O43252 (Homo sapiens)
Go to Gene View: PAPSS1
Go to UniProtKB:  O43252
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.210α = 90.00
b = 82.550β = 105.10
c = 133.600γ = 90.00
Software Package:
Software NamePurpose
X-GENdata reduction
XDSdata scaling
XFITdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-03-06
    Type: Advisory, Other
  • Version 1.4: 2017-10-11
    Type: Advisory, Refinement description