4TMT

Translation initiation factor eIF5B (517-858) mutant D533A from C. thermophilum, bound to GTPgammaS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    4TMV, 4TMW, 4TMX, 4TMZ, 4TN1, 4TMT

  • 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 govern the function of trGTPases remain poorly understood ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
eIF5BA, B345Chaetomium thermophilumMutation(s): 0 
EC: 3.6.5.3
UniProt
Find proteins for G0S8G9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S8G9 
Go to UniProtKB:  G0S8G9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSP (Subject of Investigation/LOI)
Query on GSP

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
DTT
Query on DTT

Download Ideal Coordinates CCD File 
K [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , N [auth B] , O [auth B] , P [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
U [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A], V [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.41α = 90
b = 115.91β = 101.37
c = 66.09γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
X-PLORmodel building
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XSCALEdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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