Hexameric APS kinase from Thiobacillus denitrificans

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity.

Gay, S.C.Segel, I.H.Fisher, A.J.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1021-1031

  • DOI: https://doi.org/10.1107/S0907444909026547
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Tbd_0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5 kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95 A resolution X-ray crystal structure reported here revealed a hexameric assembly with D(3) symmetry. Each subunit contains a large N-terminal sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharomyces cerevisiae, which also exhibit a hexameric assembly. However, the T. denitrificans enzyme exhibits numerous structural and sequence differences in the N-terminal domain that render it inactive with respect to ATP sulfurylase activity. Surprisingly, the C-terminal domain does indeed display APS kinase activity, indicating that this gene product is a true APS kinase. Therefore, these results provide the first structural insights into a unique hexameric APS kinase that contains a nonfunctional ATP sulfurylase-like domain of unknown function.

  • Organizational Affiliation

    Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfate adenylyltransferase, adenylylsulfate kinase
A, B, C
552Thiobacillus denitrificansMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q3SM86 (Thiobacillus denitrificans (strain ATCC 25259))
Explore Q3SM86 
Go to UniProtKB:  Q3SM86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SM86
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.071α = 90
b = 227.211β = 90
c = 106.766γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description