Crystal Structure of Bacterial ATP Sulfurylase from the Riftia pachyptila Symbiont

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

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Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila.

Beynon, J.D.MacRae, I.J.Huston, S.L.Nelson, D.C.Segel, I.H.Fisher, A.J.

(2001) Biochemistry 40: 14509-14517

  • DOI: https://doi.org/10.1021/bi015643l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In sulfur chemolithotrophic bacteria, the enzyme ATP sulfurylase functions to produce ATP and inorganic sulfate from APS and inorganic pyrophosphate, which is the final step in the biological oxidation of hydrogen sulfide to sulfate. The giant tubeworm, Riftia pachyptila, which lives near hydrothermal vents on the ocean floor, harbors a sulfur chemolithotroph as an endosymbiont in its trophosome tissue. This yet-to-be-named bacterium was found to contain high levels of ATP sulfurylase that may provide a substantial fraction of the organisms ATP. We present here, the crystal structure of ATP sulfurylase from this bacterium at 1.7 A resolution. As predicted from sequence homology, the enzyme folds into distinct N-terminal and catalytic domains, but lacks the APS kinase-like C-terminal domain that is present in fungal ATP sulfurylase. The enzyme crystallizes as a dimer with one subunit in the crystallographic asymmetric unit. Many buried solvent molecules mediate subunit contacts at the interface. Despite the high concentration of sulfate needed for crystallization, no ordered sulfate was observed in the sulfate-binding pocket. The structure reveals a mobile loop positioned over the active site. This loop is in a "closed" or "down" position in the reported crystal structures of fungal ATP sulfurylases, which contained bound substrates, but it is in an "open" or "up" position in the ligand-free Riftia symbiont enzyme. Thus, closure of the loop correlates with occupancy of the active site, although the loop itself does not interact directly with bound ligands. Rather, it appears to assist in the orientation of residues that do interact with active-site ligands. Amino acid differences between the mobile loops of the enzymes from sulfate assimilators and sulfur chemolithotrophs may account for the significant kinetic differences between the two classes of ATP sulfurylase.

  • Organizational Affiliation

    Department of Chemistry, Section of Molecular and Cellular Biology, Davis, California 95616, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SULFATE ADENYLYLTRANSFERASE396sulfur-oxidizing endosymbiont of Riftia pachyptilaMutation(s): 0 
Find proteins for Q54506 (Riftia pachyptila sulfur-oxidizing endosymbiont)
Explore Q54506 
Go to UniProtKB:  Q54506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54506
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
E [auth A],
I [auth A]
O4 S
Query on BR

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth A]
G [auth A]
H [auth A]
C [auth A],
D [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.561α = 90
b = 75.546β = 90
c = 95.853γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations