8S5S | pdb_00008s5s

Crystal structure of a Sulfite dehydrogenase from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.192 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.176 (DCC) 

Starting Model: experimental
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Literature

Structural and Spectroscopic Investigations of pH-Dependent Mo(V) Species in a Bacterial Sulfite-Oxidizing Enzyme.

Djeghader, A.Rendon, J.Biaso, F.Gerbaud, G.Nitschke, W.Schoepp-Cothenet, B.Soulimane, T.Grimaldi, S.

(2024) Inorg Chem 63: 22699-22711

  • DOI: https://doi.org/10.1021/acs.inorgchem.4c02584
  • Primary Citation of Related Structures:  
    8S5S

  • PubMed Abstract: 

    Mono-pyranopterin-containing sulfite-oxidizing enzymes (SOEs), including eukaryotic sulfite oxidases and homologous prokaryotic sulfite dehydrogenases (SDHs), are molybdenum enzymes that exist in almost all forms of life, where they catalyze the direct oxidation of sulfite into sulfate, playing a key role in protecting cells and organisms against sulfite-induced damage. To decipher their catalytic mechanism, we have previously provided structural and spectroscopic evidence for direct coordination of HPO 4 2- to the Mo atom at the active site of the SDH from the hyperthermophilic bacterium Thermus thermophilus ( Tt SDH), mimicking the proposed sulfate-bound intermediate proposed to be formed during catalysis. In this work, by solving the X-ray crystallographic structure of the unbound enzyme, we resolve the changes in the hydrogen bonding network in the molybdenum environment that enable the stabilization of the previously characterized phosphate adduct. In addition, electron paramagnetic resonance spectroscopic study of the enzyme over a wide pH range reveals the formation of pH-dependent Mo(V) species, a characteristic feature of eukaryotic SOEs. The combined use of HYSCORE, H 2 O/D 2 O exchange, and density functional theory calculations allows the detailed characterization of a typical low pH Mo(V) species previously unreported in bacterial SOEs, underlining the conservation of the active site properties of SOEs irrespective of their source organism.


  • Organizational Affiliation

    Department of Chemical Sciences and Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putaitve sulfite oxidase386Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1325
UniProt
Find proteins for Q5SIP4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIP4 
Go to UniProtKB:  Q5SIP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIP4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.192 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.176 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.02α = 90
b = 130.02β = 90
c = 114.79γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MSSClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references