Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.97 kDa 
• Atom Count: 4383 
• Modelled Residue Count: 530 
• Deposited Residue Count: 552 
• Unique protein chains: 2

2B7B

Yeast guanine nucleotide exchange factor eEF1Balpha K205A mutant in complex with eEF1A and GDP

• PDB DOI: 10.2210/pdb2B7B/pdb

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-10-04 Released: 2006-05-02 
• Deposition Author(s): Pittman, Y.R., Valente, L., Jeppesen, M.G., Andersen, G.R., Patel, S., Kinzy, T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 

Literature

Mg2+ and a key lysine modulate exchange activity of eukaryotic translation elongation factor 1B alpha

Pittman, Y.R., Valente, L., Jeppesen, M.G., Andersen, G.R., Patel, S., Kinzy, T.G.

(2006) J Biol Chem 281: 19457-19468

• PubMed: 16675455 
• DOI: 10.1074/jbc.M601076200
• Primary Citation of Related Structures:  
  2B7B, 2B7C


• PubMed Abstract: 
  

To sustain efficient translation, eukaryotic elongation factor B alpha (eEF1B alpha) functions as the guanine nucleotide exchange factor for eEF1A. Stopped-flow kinetics using 2'-(or 3')-O-N-methylanthraniloyl (mant)-GDP showed spontaneous release of nucleotide from eEF1A is extremely slow and accelerated 700-fold by eEF1B alpha. The eEF1B alpha-stimulated reaction was inhibited by Mg2+ with a K(1/2) of 3.8 mM. Previous structural studies predicted the Lys-205 residue of eEF1B alpha plays an important role in promoting nucleotide exchange by disrupting the Mg2+ binding site. Co-crystal structures of the lethal K205A mutant in the catalytic C terminus of eEF1B alpha with eEF1A and eEF1A.GDP established that the lethality was not due to a structural defect. Instead, the K205A mutant drastically reduced the nucleotide exchange activity even at very low concentrations of Mg2+. A K205R eEF1B alpha mutant on the other hand was functional in vivo and showed nearly wild-type nucleotide dissociation rates but almost no sensitivity to Mg2+. These results indicate the significant role of Mg2+ in the nucleotide exchange reaction by eEF1B alpha and establish the catalytic function of Lys-205 in displacing Mg2+ from its binding site.

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Related Citations: 

• Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha
  Andersen, G.R., Pedersen, L., Valente, L., Chatterjee, I., Kinzy, T.G., Kjeldgaard, M., Nyborg, J.
  (2000) Mol Cell 6: 1261

• Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex
  Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G., Nyborg, J.
  (2001) Nat Struct Biol 8: 531

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Organizational Affiliation: 

Department of Molecular Genetics, Microbiology & Immunology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway 08854, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 1-alpha	A	458	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02994 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02994  Go to UniProtKB:  P02994

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
elongation factor-1 beta	B	94	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: TEF5
UniProt
Find proteins for P32471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32471  Go to UniProtKB:  P32471

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.220 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.9	α = 90
b = 91.23	β = 90
c = 93.47	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-04 
• Released Date: 2006-05-02 
Deposition Author(s): Pittman, Y.R., Valente, L., Jeppesen, M.G., Andersen, G.R., Patel, S., Kinzy, T.G.

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations