Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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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: https://doi.org/10.1016/j.jmb.2005.01.005
  • Primary Citation of Related Structures:  
    1X6V, 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1A [auth B],
B [auth A]
630Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43252 (Homo sapiens)
Explore O43252 
Go to UniProtKB:  O43252
PHAROS:  O43252
GTEx:  ENSG00000138801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43252
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.5α = 90
b = 82.5β = 105
c = 133γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
XDSdata reduction
XFITdata reduction
X-GENdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description