Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 60968.55 
• Atom Count: 4115 
• Residue Count: 552 
• Unique protein chains: 2

2B7B

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

• DOI: 10.2210/pdb2B7B/pdb

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• 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: 2.6 Å
• R-Value Free: 0.291 
• R-Value Work: 0.220 

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:  
  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.Mol.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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Elongation factor 1-alpha	A	458	Saccharomyces 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
Molecule	Chains	Sequence Length	Organism	Details
elongation factor-1 beta	B	94	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 1  Gene Names: EFB1 (TEF5)
Find proteins for P32471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P32471

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.291 
• R-Value Work: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 63.900	α = 90.00
b = 91.230	β = 90.00
c = 93.470	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance