5WA0

Crystal Structure of the sulfite dehydrogenase, SorT R78Q mutant from Sinorhizobium meliloti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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


Literature

The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions.

Hsiao, J.C.McGrath, A.P.Kielmann, L.Kalimuthu, P.Darain, F.Bernhardt, P.V.Harmer, J.Lee, M.Meyers, K.Maher, M.J.Kappler, U.

(2017) Biochim Biophys Acta 1859: 19-27

  • DOI: https://doi.org/10.1016/j.bbabio.2017.10.001
  • Primary Citation of Related Structures:  
    5K3X, 5WA0

  • PubMed Abstract: 

    A central conserved arginine, first identified as a clinical mutation leading to sulfite oxidase deficiency, is essential for catalytic competency of sulfite oxidizing molybdoenzymes, but the molecular basis for its effects on turnover and substrate affinity have not been fully elucidated. We have used a bacterial sulfite dehydrogenase, SorT, which lacks an internal heme group, but transfers electrons to an external, electron accepting cytochrome, SorU, to investigate the molecular functions of this arginine residue (Arg78). Assay of the SorT Mo centre catalytic competency in the absence of SorU showed that substitutions in the central arginine (R78Q, R78K and R78M mutations) only moderately altered SorT catalytic properties, except for R78M which caused significant reduction in SorT activity. The substitutions also altered the Mo-centre redox potentials (Mo VI/V potential lowered by ca. 60-80mV). However, all Arg78 mutations significantly impaired the ability of SorT to transfer electrons to SorU, where activities were reduced 17 to 46-fold compared to SorT WT , precluding determination of kinetic parameters. This was accompanied by the observation of conformational changes in both the introduced Gln and Lys residues in the crystal structure of the enzymes. Taking into account data collected by others on related SOE mutations we propose that the formation and maintenance of an electron transfer complex between the Mo centre and electron accepting heme groups is the main function of the central arginine, and that the reduced turnover and increases in K Msulfite are caused by the inefficient operation of the oxidative half reaction of the catalytic cycle in enzymes carrying these mutations.


  • Organizational Affiliation

    Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative sulfite oxidase
A, B, C, D
365Sinorhizobium meliloti 1021Mutation(s): 1 
Gene Names: SMc04049
EC: 1.8.3.1
UniProt
Find proteins for Q92M24 (Rhizobium meliloti (strain 1021))
Explore Q92M24 
Go to UniProtKB:  Q92M24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92M24
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.52α = 90
b = 91.78β = 90.56
c = 109.67γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-10-25 
  • Deposition Author(s): Maher, M.J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description