2YAX

IODOACETAMIDE INHIBITED SULFUR OXYGENASE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens.

Veith, A.Urich, T.Seyfarth, K.Protze, J.Frazao, C.Kletzin, A.

(2011) Front Microbiol 2: 37

  • DOI: https://doi.org/10.3389/fmicb.2011.00037
  • Primary Citation of Related Structures:  
    2YAV, 2YAW, 2YAX

  • PubMed Abstract: 

    The sulfur oxygenase reductase (SOR) is the initial enzyme of the sulfur oxidation pathway in the thermoacidophilic Archaeon Acidianus ambivalens. The SOR catalyzes an oxygen-dependent sulfur disproportionation to H(2)S, sulfite and thiosulfate. The spherical, hollow, cytoplasmic enzyme is composed of 24 identical subunits with an active site pocket each comprising a mononuclear non-heme iron site and a cysteine persulfide. Substrate access and product exit occur via apolar chimney-like protrusions at the fourfold symmetry axes, via narrow polar pores at the threefold symmetry axes and via narrow apolar pores within in each subunit. In order to investigate the function of the pores we performed site-directed mutagenesis and inhibitor studies. Truncation of the chimney-like protrusions resulted in an up to sevenfold increase in specific enzyme activity compared to the wild type. Replacement of the salt bridge-forming Arg(99) residue by Ala at the threefold symmetry axes doubled the activity and introduced a bias toward reduced reaction products. Replacement of Met(296) and Met(297), which form the active site pore, lowered the specific activities by 25-55% with the exception of an M(296)V mutant. X-ray crystallography of SOR wild type crystals soaked with inhibitors showed that Hg(2+) and iodoacetamide (IAA) bind to cysteines within the active site, whereas Zn(2+) binds to a histidine in a side channel of the enzyme. The Zn(2+) inhibition was partially alleviated by mutation of the His residue. The expansion of the pores in the outer shell led to an increased enzyme activity while the integrity of the active site pore seems to be important. Hg(2+) and IAA block cysteines in the active site pocket, while Zn(2+) interferes over a distance, possibly by restriction of protein flexibility or substrate access or product exit.


  • Organizational Affiliation

    Institute of Microbiology and Genetics, Technische Universität Darmstadt Darmstadt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SULFUR OXYGENASE/REDUCTASE
A, D, E
318Acidianus ambivalensMutation(s): 0 
EC: 1.13.11.55
UniProt
Find proteins for P29082 (Acidianus ambivalens)
Explore P29082 
Go to UniProtKB:  P29082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29082
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SULFUR OXYGENASE/REDUCTASE
B, C, F
318Acidianus ambivalensMutation(s): 0 
EC: 1.13.11.55
UniProt
Find proteins for P29082 (Acidianus ambivalens)
Explore P29082 
Go to UniProtKB:  P29082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29082
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.897α = 90
b = 161.897β = 90
c = 154.273γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description