spacer
spacer

PDBsum entry 1g7c
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Translation PDB id
1g7c

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
440 a.a. *
90 a.a. *
Ligands
5GP
Waters ×448
* Residue conservation analysis
PDB id:
1g7c
Name: Translation
Title: Yeast eef1a:eef1ba in complex with gdpnp
Structure: Elongation factor 1-alpha. Chain: a. Synonym: eef1a. Elongation factor 1-beta. Chain: b. Fragment: c-terminal domain. Synonym: eef1ba. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: tky331. Gene: tef5. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.05Å     R-factor:   0.208     R-free:   0.231
Authors: G.R.Andersen,L.Valente,L.Pedersen,T.G.Kinzy,J.Nyborg
Key ref:
G.R.Andersen et al. (2001). Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex. Nat Struct Biol, 8, 531-534. PubMed id: 11373622 DOI: 10.1038/88598
Date:
10-Nov-00     Release date:   06-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02994  (EF1A_YEAST) -  Elongation factor 1-alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		458 a.a.
440 a.a.
Protein chain
Pfam   ArchSchema ?
P32471  (EF1B_YEAST) -  Elongation factor 1-beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		206 a.a.
90 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/88598 Nat Struct Biol 8:531-534 (2001)
PubMed id: 11373622  
 
 
Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex.
G.R.Andersen, L.Valente, L.Pedersen, T.G.Kinzy, J.Nyborg.
 
  ABSTRACT  
 
In the elongation cycle of protein biosynthesis, the nucleotide exchange factor eEF1Balpha catalyzes the exchange of GDP bound to the G-protein, eEF1A, for GTP. To obtain more information about the recently solved eEF1A-eEF1Balpha structure, we determined the structures of the eEF1A-eEF1Balpha-GDP-Mg2+, eEF1A-eEF1Balpha-GDP and eEF1A-eEF1Balpha-GDPNP complexes at 3.0, 2.4 and 2.05 A resolution, respectively. Minor changes, specifically around the nucleotide binding site, in eEF1A and eEF1Balpha are consistent with in vivo data. The base, sugar and alpha-phosphate bind as in other known nucleotide G-protein complexes, whereas the beta- and gamma-phosphates are disordered. A mutation of Lys 205 in eEF1Balpha that inserts into the Mg2+ binding site of eEF1A is lethal. This together with the structures emphasizes the essential role of Mg2+ in nucleotide exchange in the eEF1A-eEF1Balpha complex.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Electron densities around the nucleotides after the final refinement. a, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDP -Mg2+ complex. The 'M' labels a residual electron density that most likely contains a Mg2+ ion. b, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDP complex. c, Sigmaa-weighted 2F[o] - F[c] electron density map contoured at 1.2 for the GDPNP complex. Water atoms are shown as red spheres. The electron densities were plotted with the map_cover option in O25 using a radius of 1.5 Å. Labels on residues in eEF1A and eEF1B are red and blue, respectively. All shown atoms were omitted from map calculations. 		Figure 2.
Figure 2. The exchange mechanism. The shown structures are EF-Tu -GDP (PDB accession code 1TUI), eEF1A -eEF1B -GDP -Mg2+ (PDB accession code 1IJF), eEF1A -eEF1B (PDB accession code 1F60), eEF1A -eEF1B -GDPNP (PDB accession code 1G7C) and EF-Tu -GDPNP (PDB accession code 1EFT). Regions around the binding site of EF-Tu -GDPNP are labeled G1 -G5 according to the nomenclature of Sprang28 and colored identically in the other structures. The G2 region, part of the switch 1 region, is only shown for the EF-Tu -GDPNP, because it is distant from the nucleotide in the other structures. Comparison with EF-Tu -GDP, EF-Tu -GDPNP and EF-Tu -EF-Ts indicate that the shown peptide in the P-loop of eEF1A is likely to flip in the exchange reaction. Mg2+ ions are shown as blue spheres.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 531-534) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
20209157 E.Greganova, M.Heller, and P.Bütikofer (2010).
A structural domain mediates attachment of ethanolamine phosphoglycerol to eukaryotic elongation factor 1A in Trypanosoma brucei.
  PLoS One, 5, e9486.  
21079685 Z.Li, J.Pogany, S.Tupman, A.M.Esposito, T.G.Kinzy, and P.D.Nagy (2010).
Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthesis.
  PLoS Pathog, 6, e1001175.  
19636410 D.C.Soares, P.N.Barlow, H.J.Newbery, D.J.Porteous, and C.M.Abbott (2009).
Structural models of human eEF1A1 and eEF1A2 reveal two distinct surface clusters of sequence variation and potential differences in phosphorylation.
  PLoS One, 4, e6315.  
19357788 G.H.Gile, D.Faktorová, C.A.Castlejohn, G.Burger, B.F.Lang, M.A.Farmer, J.Lukes, and P.J.Keeling (2009).
Distribution and phylogeny of EFL and EF-1alpha in Euglenozoa suggest ancestral co-occurrence followed by differential loss.
  PLoS ONE, 4, e5162.  
19095653 Y.R.Pittman, K.Kandl, M.Lewis, L.Valente, and T.G.Kinzy (2009).
Coordination of Eukaryotic Translation Elongation Factor 1A (eEF1A) Function in Actin Organization and Translation Elongation by the Guanine Nucleotide Exchange Factor eEF1B{alpha}.
  J Biol Chem, 284, 4739-4747.  
18499667 A.Signorell, J.Jelk, M.Rauch, and P.Bütikofer (2008).
Phosphatidylethanolamine is the precursor of the ethanolamine phosphoglycerol moiety bound to eukaryotic elongation factor 1A.
  J Biol Chem, 283, 20320-20329.  
18221514 D.S.Kanibolotsky, O.V.Novosyl'na, C.M.Abbott, B.S.Negrutskii, and A.V.El'skaya (2008).
Multiple molecular dynamics simulation of the isoforms of human translation elongation factor 1A reveals reversible fluctuations between "open" and "closed" conformations and suggests specific for eEF1A1 affinity for Ca2+-calmodulin.
  BMC Struct Biol, 8, 4.  
18459963 K.Koiwai, S.Maezawa, T.Hayano, M.Iitsuka, and O.Koiwai (2008).
BPOZ-2 directly binds to eEF1A1 to promote eEF1A1 ubiquitylation and degradation and prevent translation.
  Genes Cells, 13, 593-607.  
18562321 S.B.Ozturk, and T.G.Kinzy (2008).
Guanine Nucleotide Exchange Factor Independence of the G-protein eEF1A through Novel Mutant Forms and Biochemical Properties.
  J Biol Chem, 283, 23244-23253.  
17218277 C.Thomas, I.Fricke, A.Scrima, A.Berken, and A.Wittinghofer (2007).
Structural evidence for a common intermediate in small G protein-GEF reactions.
  Mol Cell, 25, 141-149.
PDB codes: 2ntx 2nty
17565370 E.P.Plant, P.Nguyen, J.R.Russ, Y.R.Pittman, T.Nguyen, J.T.Quesinberry, T.G.Kinzy, and J.D.Dinman (2007).
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
  PLoS ONE, 2, e517.  
17925388 K.B.Gromadski, T.Schümmer, A.Strømgaard, C.R.Knudsen, T.G.Kinzy, and M.V.Rodnina (2007).
Kinetics of the interactions between yeast elongation factors 1A and 1Balpha, guanine nucleotides, and aminoacyl-tRNA.
  J Biol Chem, 282, 35629-35637.  
17178834 S.R.Gross, and T.G.Kinzy (2007).
Improper organization of the actin cytoskeleton affects protein synthesis at initiation.
  Mol Cell Biol, 27, 1974-1989.  
16541104 A.Itzen, O.Pylypenko, R.S.Goody, K.Alexandrov, and A.Rak (2006).
Nucleotide exchange via local protein unfolding--structure of Rab8 in complex with MSS4.
  EMBO J, 25, 1445-1455.
PDB code: 2fu5
16954224 M.Anand, B.Balar, R.Ulloque, S.R.Gross, and T.G.Kinzy (2006).
Domain and nucleotide dependence of the interaction between Saccharomyces cerevisiae translation elongation factors 3 and 1A.
  J Biol Chem, 281, 32318-32326.  
16951075 S.B.Ozturk, M.R.Vishnu, O.Olarewaju, L.M.Starita, D.C.Masison, and T.G.Kinzy (2006).
Unique classes of mutations in the Saccharomyces cerevisiae G-protein translation elongation factor 1A suppress the requirement for guanine nucleotide exchange.
  Genetics, 174, 651-663.  
16675455 Y.R.Pittman, L.Valente, M.G.Jeppesen, G.R.Andersen, S.Patel, and T.G.Kinzy (2006).
Mg2+ and a key lysine modulate exchange activity of eukaryotic translation elongation factor 1B alpha.
  J Biol Chem, 281, 19457-19468.
PDB codes: 2b7b 2b7c
14978301 C.Blouin, D.Butt, and A.J.Roger (2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
  Protein Sci, 13, 608-616.  
15189156 L.D.Kapp, and J.R.Lorsch (2004).
The molecular mechanics of eukaryotic translation.
  Annu Rev Biochem, 73, 657-704.  
15341733 T.Ito, A.Marintchev, and G.Wagner (2004).
Solution structure of human initiation factor eIF2alpha reveals homology to the elongation factor eEF1B.
  Structure, 12, 1693-1704.
PDB code: 1q8k
14623968 C.Cans, B.J.Passer, V.Shalak, V.Nancy-Portebois, V.Crible, N.Amzallag, D.Allanic, R.Tufino, M.Argentini, D.Moras, G.Fiucci, B.Goud, M.Mirande, R.Amson, and A.Telerman (2003).
Translationally controlled tumor protein acts as a guanine nucleotide dissociation inhibitor on the translation elongation factor eEF1A.
  Proc Natl Acad Sci U S A, 100, 13892-13897.  
14690595 E.Mossessova, R.A.Corpina, and J.Goldberg (2003).
Crystal structure of ARF1*Sec7 complexed with Brefeldin A and its implications for the guanine nucleotide exchange mechanism.
  Mol Cell, 12, 1403-1411.
PDB code: 1re0
12932732 G.R.Andersen, P.Nissen, and J.Nyborg (2003).
Elongation factors in protein biosynthesis.
  Trends Biochem Sci, 28, 434-441.  
12493761 M.Anand, K.Chakraburtty, M.J.Marton, A.G.Hinnebusch, and T.G.Kinzy (2003).
Functional interactions between yeast translation eukaryotic elongation factor (eEF) 1A and eEF3.
  J Biol Chem, 278, 6985-6991.  
12909337 P.R.Copeland (2003).
Regulation of gene expression by stop codon recoding: selenocysteine.
  Gene, 312, 17-25.  
12692531 R.Jørgensen, P.A.Ortiz, A.Carr-Schmid, P.Nissen, T.G.Kinzy, and G.R.Andersen (2003).
Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase.
  Nat Struct Biol, 10, 379-385.
PDB codes: 1n0u 1n0v
12920118 S.Vanwetswinkel, J.Kriek, G.R.Andersen, P.Güntert, J.Dijk, G.W.Canters, and G.Siegal (2003).
Solution structure of the 162 residue C-terminal domain of human elongation factor 1Bgamma.
  J Biol Chem, 278, 43443-43451.  
12853641 Y.Inagaki, C.Blouin, E.Susko, and A.J.Roger (2003).
Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria.
  Nucleic Acids Res, 31, 4227-4237.  
12356745 E.Gomez, S.S.Mohammad, and G.D.Pavitt (2002).
Characterization of the minimal catalytic domain within eIF2B: the guanine-nucleotide exchange factor for translation initiation.
  EMBO J, 21, 5292-5301.  
11927566 E.Schmitt, S.Blanquet, and Y.Mechulam (2002).
The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
  EMBO J, 21, 1821-1832.
PDB codes: 1kjz 1kk0 1kk1 1kk2 1kk3
12217519 J.W.Harger, A.Meskauskas, and J.D.Dinman (2002).
An "integrated model" of programmed ribosomal frameshifting.
  Trends Biochem Sci, 27, 448-454.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
11701921 I.R.Vetter, and A.Wittinghofer (2001).
The guanine nucleotide-binding switch in three dimensions.
  Science, 294, 1299-1304.  
11574461 L.Vitagliano, M.Masullo, F.Sica, A.Zagari, and V.Bocchini (2001).
The crystal structure of Sulfolobus solfataricus elongation factor 1alpha in complex with GDP reveals novel features in nucleotide binding and exchange.
  EMBO J, 20, 5305-5311.
PDB code: 1jny
12762046 M.Anand, L.Valente, A.Carr-Schmid, R.Munshi, O.Olarewaju, P.A.Ortiz, and T.G.Kinzy (2001).
Translation elongation factor 1 functions in the yeast Saccharomyces cerevisiae.
  Cold Spring Harb Symp Quant Biol, 66, 439-448.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer
spacer