4Y27

E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.998 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis.

Koch, M.Flur, S.Kreutz, C.Ennifar, E.Micura, R.Polacek, N.

(2015) Proc.Natl.Acad.Sci.USA 112: E2561-E2568

  • DOI: 10.1073/pnas.1505231112

  • PubMed Abstract: 
  • Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide eviden ...

    Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
27-mer SRL RNAA27Escherichia coli
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
OMG
Query on OMG
A
RNA LINKINGC11 H16 N5 O8 PG
45A
Query on 45A
A
NON-POLYMERC11 H16 N5 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.998 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.135 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 29.500α = 90.00
b = 29.500β = 90.00
c = 77.150γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_143388/1
Austrian Science FoundationAustriaP21641
Austrian Science FoundationAustriaI1040

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release