5VE5

Crystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese domain inactivating mutation (C314S) from Burkholderia phytofirmans in complex with glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation.

Motl, N.Skiba, M.A.Kabil, O.Smith, J.L.Banerjee, R.

(2017) J. Biol. Chem. 292: 14026-14038

  • DOI: 10.1074/jbc.M117.790170
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodane ...

    Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.


    Organizational Affiliation

    From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BpPRF
A, B, C
377Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)Mutation(s): 1 
Find proteins for B2TEQ2 (Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN))
Go to UniProtKB:  B2TEQ2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A, B, C
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
A, C
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.503α = 90.00
b = 83.503β = 90.00
c = 547.609γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM112455
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM008353

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Database references