2BM0

Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutant T84A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Insights Into Fusidic Acid Resistance and Sensitivity in EF-G

Hansson, S.Singh, R.Gudkov, A.T.Liljas, A.Logan, D.T.

(2005) J.Mol.Biol. 348: 939

  • DOI: 10.1016/j.jmb.2005.02.066
  • Primary Citation of Related Structures:  
  • Also Cited By: 2BV3

  • PubMed Abstract: 
  • Fusidic acid (FA) is a steroid antibiotic commonly used against Gram positive bacterial infections. It inhibits protein synthesis by stalling elongation factor G (EF-G) on the ribosome after translocation. A significant number of the mutations confer ...

    Fusidic acid (FA) is a steroid antibiotic commonly used against Gram positive bacterial infections. It inhibits protein synthesis by stalling elongation factor G (EF-G) on the ribosome after translocation. A significant number of the mutations conferring strong FA resistance have been mapped at the interfaces between domains G, III and V of EF-G. However, direct information on how such mutations affect the structure has hitherto not been available. Here we present the crystal structures of two mutants of Thermus thermophilus EF-G, G16V and T84A, which exhibit FA hypersensitivity and resistance in vitro, respectively. These mutants also have higher and lower affinity for GTP respectively than wild-type EF-G. The mutations cause significant conformational changes in the switch II loop that have opposite effects on the position of a key residue, Phe90, which undergoes large conformational changes. This correlates with the importance of Phe90 in FA sensitivity reported in previous studies. These structures substantiate the importance of the domain G/domain III/domain V interfaces as a key component of the FA binding site. The mutations also cause subtle changes in the environment of the "P-loop lysine", Lys25. This led us to examine the conformation of the equivalent residue in all structures of translational GTPases, which revealed that EF-G and eEF2 form a group separate from the others and suggested that the role of Lys25 may be different in the two groups.


    Related Citations: 
    • Three-Dimensional Structure of the Ribosomal Translocase: Elongation Factor G from Thermus Thermophilus
      Aevarsson, A.,Brazhnikov, E.,Garber, M.,Zheltonosova, J.,Chirgadze, Y.,Al-Karadaghi, S.,Svensson, L.A.,Liljas, A.
      (1994) Embo J. 13: 3669
    • The Structure of Elongation Factor G in Complex with Gdp: Conformational Flexibility and Nucleotide Exchange
      Al-Karadaghi, S.,Aevarsson, A.,Garber, M.,Zheltonosova, J.,Liljas, A.
      (1996) Structure 4: 555
    • Mutations in the G-Domain of Elongation Factor G from Thermus Thermophilus Affect Both its Interaction with GTP and Fusidic Acid.
      Martemyanov, K.A.,Liljas, A.,Yarunin, A.S.,Gudkov, A.T.
      (2001) J.Biol.Chem. 276: 28774
    • Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site
      Laurberg, M.,Kristensen, O.,Martemyanov, K.,Gudkov, A.T.,Nagaev, I.,Hughes, D.,Liljas, A.
      (2000) J.Mol.Biol. 303: 593
    • The Crystal Structure of Elongation Factor G Complexed with Gdp, at 2.7 A Resolution
      Czworkowski, J.,Wang, J.,Steitz, T.A.,Moore, P.B.
      (1994) Embo J. 13: 3661


    Organizational Affiliation

    Department of Molecular Biophysics, Lund University, Box 124, S-221 00 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR G
A
691Thermus thermophilusMutation(s): 1 
Gene Names: fusA (fus)
Find proteins for P13551 (Thermus thermophilus)
Go to UniProtKB:  P13551
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKi: 440000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.200α = 90.00
b = 88.500β = 90.00
c = 116.900γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CCP4phasing
MOLREPphasing
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection