1XJQ | pdb_00001xjq

ADP Complex OF HUMAN PAPS SYNTHETASE 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1XJQ

Ligand Structure Quality Assessment 


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 Biology 347: 623-635

  • DOI: https://doi.org/10.1016/j.jmb.2005.01.005
  • Primary Citation 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

Macromolecule Content 

  • Total Structure Weight: 144.68 kDa 
  • Atom Count: 9,997 
  • Modeled Residue Count: 1,153 
  • Deposited Residue Count: 1,260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1A [auth B],
B [auth A]
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
GTEx:  ENSG00000138801 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43252
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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

View Full Validation Report



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
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description