8QUA

GTP binding protein YsxC from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of GTPase YsxC from Staphylococcus aureus.

Biktimirov, A.Islamov, D.Fatkhullin, B.Lazarenko, V.Validov, S.Yusupov, M.Usachev, K.

(2024) Biochem Biophys Res Commun 699: 149545-149545

  • DOI: https://doi.org/10.1016/j.bbrc.2024.149545
  • Primary Citation of Related Structures:  
    8QUA

  • PubMed Abstract: 

    The YsxC protein from Staphylococcus aureus is a GTP-binding protein from the TRAFAC superfamily of the TrmE-Era-EngA-EngB-Septin-like GTPase class, EngB family of GTPases. Recent structural and biochemical studies of YsxC function show that it is an integral part of the pathogenic microorganism life cycle, as it is involved in the assembly of the large 50S ribosomal subunit. Structural studies of this protein with its specific functional features make it an attractive target for further development of new selective antimicrobials. In this study, we cloned the ysxC protein gene from S. aureus, overexpressed the protein in E. coli, and subsequently purified and crystallized it. Protein crystals were successfully grown using the vapor diffusion method, yielding diffraction data with a resolution of up to 2 Å. Comparative analysis of the structure of SaYsxC with known three-dimensional structures of homologs from other microorganisms showed the presence of structural differences for the apo form.


  • Organizational Affiliation

    Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable GTP-binding protein EngB196Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: engB
UniProt
Find proteins for A5ITJ8 (Staphylococcus aureus (strain JH9))
Explore A5ITJ8 
Go to UniProtKB:  A5ITJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5ITJ8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.942α = 90
b = 55.942β = 90
c = 107.112γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
CrysalisProdata collection
Cootmodel building
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation21-74-20034

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release