9JKP | pdb_00009jkp

Crystal structure of the Staphylococcus aureus GTPase Era in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb9JKP/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-16 Released: 2024-12-18 
• Deposition Author(s): Klochkova, E., Biktimirov, A., Islamov, D., Belousov, A., Yusupov, M., Usachev, K.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 

Starting Model: in silico

Literature

Crystal structure of the GDP-bound GTPase Era from Staphylococcus aureus.

Klochkova, E., Biktimirov, A., Islamov, D., Belousov, A., Validov, S., Yusupov, M., Usachev, K.

(2024) Biochem Biophys Res Commun 735: 150852-150852

• PubMed: 39432921 
• DOI: https://doi.org/10.1016/j.bbrc.2024.150852
• Primary Citation of Related Structures:  
  9JKP


• PubMed Abstract: 
  

  GTPase Era from Staphylococcus aureus belongs to the TRAFAC superfamily of the TrmE-Era-EngA-EngB-Septin-like GTPases class and plays a significant role in the vital activity of this pathogenic microorganism as a maturation factor of the 30S ribosome subunit. However, the functions of this protein are not fully understood, making it a promising object for further study. Here, the 2.76 Å resolution crystal structure of Staphylococcus aureus Era in complex with GDP is presented. Structural comparison with other GTP-bound and GDP-bound homologous proteins, GTPase domain and the KH domain revealed a mutual orientation in S. aureus which has not been described before. The GDP-bound Era structure presented here will facilitate efforts to elucidate its interactions with its regulators and lay the foundation for a structure-based search for specific inhibitors.

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Organizational Affiliation: 
• Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation.
Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation; Sao Carlos Institute of Physics, University of Sao Paulo, poloTErRA, 13563-120, Sao Carlos, São Paolo, Brazil.
Federal Research Center «Kazan Scientific Center of Russian Academy of Sciences», Kazan, 420111, Russian Federation.
National Research Centre Kurchatov Institute, Kurchatov Sq. 2, 123182, Moscow, Russian Federation; Institute of Genetics, Molecular and Cellular Biology, CNRS UMR7104, INSERM U964, Universit'e de Strasbourg, Illkirch, F-67400, France.
Kazan Federal University, 18 Kremlyovskaya St., 420008, Kazan, Russian Federation. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.85 kDa 
• Atom Count: 2,450 
• Modeled Residue Count: 299 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase Era	A [auth B]	300	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: era, SAOUHSC_01668
UniProt
Find proteins for Q2FY06 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FY06  Go to UniProtKB:  Q2FY06

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.146	α = 90
b = 78.146	β = 90
c = 244.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Klochkova, E., Biktimirov, A., Islamov, D., Belousov, A., Yusupov, M., Usachev, K.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	21-74-20034

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release