5VE3

Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein from Burkholderia phytofirmans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5VE3, 5VE4, 5VE5

  • PubMed Abstract: 
  • Hydrogen sulfide (H 2 S) 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 H 2 S to thiosulfate and sulfate ...

    Hydrogen sulfide (H 2 S) 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 H 2 S 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 rbanerje@umich.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BpPRFB [auth A], A [auth B]373Paraburkholderia phytofirmans PsJNMutation(s): 0 
Gene Names: Bphyt_4191
EC: 1.13.11.18 (PDB Primary Data), 2.8.1.1 (PDB Primary Data)
UniProt
Find proteins for B2TEQ2 (Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN))
Explore B2TEQ2 
Go to UniProtKB:  B2TEQ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth B], D [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A [auth B], B [auth A]L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.689α = 90
b = 108.333β = 90
c = 119.616γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BALBESphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM112455
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008353

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence