4TMX

Translation initiation factor eIF5B (517-858) mutant D533N from C. thermophilum, bound to GTP and sodium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A monovalent cation acts as structural and catalytic cofactor in translational GTPases.

Kuhle, B.Ficner, R.

(2014) Embo J. 33: 2547-2563

  • DOI: 10.15252/embj.201488517
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany.,Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany bkuhle@gwdg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
eIF5B
A, B
345Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
EC: 3.6.5.3
Find proteins for G0S8G9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S8G9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.530α = 90.00
b = 116.820β = 101.02
c = 66.490γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
XSCALEdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-06-02 
  • Released Date: 2014-09-24 
  • Deposition Author(s): Kuhle, B., Ficner, R.

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-11-19
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references
  • Version 1.3: 2016-02-24
    Type: Structure summary