8YRC | pdb_00008yrc

Chlorinated YabJ from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Literature

YabJ from Staphylococcus aureus entraps chlorides within its pocket.

Jeong, C.Kim, H.J.

(2024) Biochem Biophys Res Commun 710: 149892-149892

  • DOI: https://doi.org/10.1016/j.bbrc.2024.149892
  • Primary Citation Related Structures: 
    8YRC

  • PubMed Abstract: 

    Chlorination is a potent disinfectant against various microorganisms, including bacteria and viruses, by inducing protein modifications and functional changes. Chlorine, in the form of sodium hypochlorite, stands out as the predominant sanitizer choice due to its cost-effectiveness and powerful antimicrobial properties. Upon exposure to chlorination, proteins undergo modifications, with amino acids experiencing alterations through the attachment of chloride or oxygen atoms. These modifications lead to shifts in protein function and the modulation of downstream signaling pathways, ultimately resulting in a bactericidal effect. However, certain survival proteins, such as chaperones or transcription factors, aid organisms in overcoming harsh chlorination conditions. The expression of YabJ, a highly conserved protein from Staphylococcus aureus, is regulated by a stress-activated sigma factor called sigma B (σB). This research revealed that S. aureus YabJ maintains its structural integrity even under intense chlorination conditions and harbors sodium hypochlorite molecules within its surface pocket. Notably, the pocket of S. aureus YabJ is primarily composed of amino acids less susceptible to chlorination-induced damage, rendering it resistant to such effects. This study elucidates how S. aureus YabJ evades the detrimental effects of chlorination and highlights its role in sequestering sodium hypochlorite within its structure. Consequently, this process enhances resilience and facilitates adaptation to challenging environmental conditions.


  • Organizational Affiliation
    • College of Pharmacy, Woosuk University, Wanju, 55338, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 42.9 kDa 
  • Atom Count: 2,994 
  • Modeled Residue Count: 374 
  • Deposited Residue Count: 390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation inhibitor homologue
A, B, C
130Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SAV0497
UniProt
Find proteins for A0A0H3JTJ5 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JTJ5 
Go to UniProtKB:  A0A0H3JTJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JTJ5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.69α = 90
b = 75.35β = 103.05
c = 52.83γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2024-04-24
    Type: Initial release