5O8W

CRYSTAL STRUCTURE ANALYSIS OF THE YEAST ELONGATION FACTOR COMPLEX EEF1A:EEF1BA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1F60 - determined by Andersen, G.R., Pedersen, L., Valente, L., Kinzy, T.G., Nyborg, J.  

Literature

Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A.

Jank, T.Belyi, Y.Wirth, C.Rospert, S.Hu, Z.Dengjel, J.Tzivelekidis, T.Andersen, G.R.Hunte, C.Schlosser, A.Aktories, K.

(2017) J. Biol. Chem. 292: 16014-16023

  • DOI: 10.1074/jbc.M117.801035

  • PubMed Abstract: 
  • Ribosomal translation factors are fundamental for protein synthesis and highly conserved in all kingdoms of life. The essential eukaryotic elongation factor 1A (eEF1A) delivers aminoacyl tRNAs to the A-site of the translating 80S ribosome. Several st ...

    Ribosomal translation factors are fundamental for protein synthesis and highly conserved in all kingdoms of life. The essential eukaryotic elongation factor 1A (eEF1A) delivers aminoacyl tRNAs to the A-site of the translating 80S ribosome. Several studies have revealed that eEF1A is posttranslationally modified. Using MS analysis, site-directed mutagenesis, and X-ray structural data analysis of Saccharomyces cerevisiae eEF1A, we identified a posttranslational modification in which the α amino group of mono-l-glutamine is covalently linked to the side chain of glutamate 45 in eEF1A. The MS analysis suggested that all eEF1A molecules are modified by this glutaminylation and that this posttranslational modification occurs at all stages of yeast growth. The mutational studies revealed that this glutaminylation is not essential for the normal functions of eEF1A in S. cerevisiae However, eEF1A glutaminylation slightly reduced growth under antibiotic-induced translational stress conditions. Moreover, we identified the same posttranslational modification in eEF1A from Schizosaccharomyces pombe but not in various other eukaryotic organisms tested despite strict conservation of the Glu45 residue among these organisms. We therefore conclude that eEF1A glutaminylation is a yeast-specific posttranslational modification that appears to influence protein translation.


    Organizational Affiliation

    From the Institute for Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany, thomas.jank@pharmakol.uni-freiburg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 1-alpha
A
466Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TEF1, TEF2
Find proteins for P02994 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02994
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 1-beta
B
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EFB1 (TEF5)
Find proteins for P32471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32471
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download SDF File 
Download CCD File 
A
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.850α = 90.00
b = 91.810β = 90.00
c = 92.980γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC746
German Federal and State GovernmentsGermanyEXC 294 BIOSS

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy
  • Version 1.3: 2019-05-08
    Type: Advisory, Data collection, Derived calculations