1XNJ

APS complex of human PAPS synthetase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.3 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, 1X6V

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1B [auth A], A [auth B]630Homo sapiensMutation(s): 0 
Gene Names: PAPSS1PAPSSATPSK1
EC: 2.7.7.4 (PDB Primary Data), 2.7.1.25 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43252 (Homo sapiens)
Explore O43252 
Go to UniProtKB:  O43252
PHAROS:  O43252
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADX (Subject of Investigation/LOI)
Query on ADX

Download Ideal Coordinates CCD File 
D [auth B], E [auth B], F [auth A]ADENOSINE-5'-PHOSPHOSULFATE
C10 H14 N5 O10 P S
IRLPACMLTUPBCL-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • 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
REFMACrefinement
X-GENdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



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