8ZBD | pdb_00008zbd

Crystal structure of Persulfide Dioxygenase from Beggiatoa leptomitoformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Literature

Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis , Where Persulfide Dioxygenase Plays a Key Role.

Rudenko, T.S.Trubitsina, L.I.Terentyev, V.V.Trubitsin, I.V.Borshchevskiy, V.I.Tishchenko, S.V.Gabdulkhakov, A.G.Leontievsky, A.A.Grabovich, M.Y.

(2024) Int J Mol Sci 25

  • DOI: https://doi.org/10.3390/ijms252010962
  • Primary Citation Related Structures: 
    8ZBD

  • PubMed Abstract: 

    Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa representatives. Annotation of the genome of Beggiatoa leptomitoformis D-402 did not identify any genes for the oxidation or reduction of elemental sulfur. By searching BLASTP, two putative persulfide dioxygenase (PDO) homologs were found in the genome of B. leptomitoformis . In some heterotrophic prokaryotes, PDO is involved in the oxidation of sulfane sulfur. According to HPLC-MS/MS, the revealed protein was reliably detected in a culture sample grown only in the presence of endogenous sulfur and CO 2 . The recombinant protein from B. leptomitoformis was active in the presence of glutathione persulfide. The crystal structure of recombinant PDO exhibited consistency with known structures of type I PDO. Thus, it was shown that B. leptomitoformis uses PDO to oxidize endogenous sulfur. Additionally, on the basis of HPLC-MS/MS, RT-qPCR, and the study of PDO reaction products, we predicted the interrelation of PDO and Sox-system function in the oxidation of endogenous sulfur in B. leptomitoformis and the connection of this process with energy metabolism.


  • Organizational Affiliation
    • Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia.

Macromolecule Content 

  • Total Structure Weight: 55.28 kDa 
  • Atom Count: 3,745 
  • Modeled Residue Count: 470 
  • Deposited Residue Count: 496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MBL fold metallo-hydrolase
A, B
248Beggiatoa leptomitoformisMutation(s): 0 
Gene Names: BLE401_10280
UniProt
Find proteins for A0A2N9YEY8 (Beggiatoa leptomitoformis)
Explore A0A2N9YEY8 
Go to UniProtKB:  A0A2N9YEY8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2N9YEY8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.997α = 90
b = 66.997β = 90
c = 245.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release