4TMX image
Entry Detail
PDB ID:
4TMX
Keywords:
Title:
Translation initiation factor eIF5B (517-858) mutant D533N from C. thermophilum, bound to GTP and sodium
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-06-02
Release Date:
2014-09-24
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:eIF5B
Mutations:D533N
Chain IDs:A, B
Chain Length:345
Number of Molecules:2
Biological Source:Chaetomium thermophilum
Primary Citation
A monovalent cation acts as structural and catalytic cofactor in translational GTPases.
Embo J. 33 2547 2563 (2014)
PMID: 25225612 DOI: 10.15252/embj.201488517

Abstact

Translational GTPases are universally conserved GTP hydrolyzing enzymes, critical for fidelity and speed of ribosomal protein biosynthesis. Despite their central roles, the mechanisms of GTP-dependent conformational switching and GTP hydrolysis that govern the function of trGTPases remain poorly understood. Here, we provide biochemical and high-resolution structural evidence that eIF5B and aEF1A/EF-Tu bound to GTP or GTPγS coordinate a monovalent cation (M(+)) in their active site. Our data reveal that M(+) ions form constitutive components of the catalytic machinery in trGTPases acting as structural cofactor to stabilize the GTP-bound "on" state. Additionally, the M(+) ion provides a positive charge into the active site analogous to the arginine-finger in the Ras-RasGAP system indicating a similar role as catalytic element that stabilizes the transition state of the hydrolysis reaction. In sequence and structure, the coordination shell for the M(+) ion is, with exception of eIF2γ, highly conserved among trGTPases from bacteria to human. We therefore propose a universal mechanism of M(+)-dependent conformational switching and GTP hydrolysis among trGTPases with important consequences for the interpretation of available biochemical and structural data.

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