9G8T | pdb_00009g8t

Crystal structure of the persulfide dioxygenase (PDO - PA2915) from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure and function of persulfide dioxygenase from Pseudomonas aeruginosa : Implications on H 2 S homeostasis and interplay with nitric oxide.

Giordano, F.Troilo, F.Nastasi, M.R.Caruso, L.Mellini, M.Travaglini-Allocatelli, C.Giardina, G.Vicente, J.B.Rampioni, G.Di Matteo, A.Forte, E.Giuffre, A.

(2026) iScience 29: 114586-114586

  • DOI: https://doi.org/10.1016/j.isci.2025.114586
  • Primary Citation Related Structures: 
    9G8T

  • PubMed Abstract: 

    Hydrogen sulfide is an important signaling molecule, beneficial at physiological concentrations but harmful at higher levels, due to which a tight control of its bioavailability is essential. Here, we investigated persulfide dioxygenase, an enzyme involved in H 2 S catabolism, from the pathogen Pseudomonas aeruginosa ( Pa PDO). Deletion of the gene pdo led to a 4-fold increase in H 2 S concentration, confirming its physiological role. The recombinant enzyme was structurally characterized at 2.06 Å resolution and assigned to the metallo-β-lactamase superfamily. Compared with its human homolog, Pa PDO displayed a different dimerization area and a larger active site, suggesting different substrate preferences. Functionally, Pa PDO catalyzed glutathione persulfide dioxygenation with a high turnover rate, and its activity was enhanced by reduced glutathione. Interestingly, the results show that Pa PDO binds to nitric oxide, which reversibly inhibits its catalytic activity. These findings reveal a novel mechanism of crosstalk between hydrogen sulfide and nitric oxide signaling and provide insights into redox regulation in a multidrug-resistant pathogen.


  • Organizational Affiliation
    • Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy.

Macromolecule Content 

  • Total Structure Weight: 33.37 kDa 
  • Atom Count: 2,284 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 296 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase domain-containing protein296Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA2915
UniProt
Find proteins for Q9HZT2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZT2 
Go to UniProtKB:  Q9HZT2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZT2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.24α = 90
b = 77.24β = 90
c = 83.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionPE00000007
Ministero dell Universita e della RicercaItaly20224BYR59
European Union (EU)European UnionIR0000009

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Database references