PDBsum entry 1paq

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Translation PDB id
Protein chain
161 a.a. *
Waters ×90
* Residue conservation analysis
PDB id:
Name: Translation
Title: Crystal structure of the catalytic fragment of eukaryotic initiation factor 2b epsilon
Structure: Translation initiation factor eif-2b epsilon subunit. Chain: a. Fragment: catalytic domain, residues (524-712). Synonym: eif-2b gdp-gtp exchange factor, guanine nucleotide exchange factor subunit gcd6, gcd complex subunit gcd6. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gcd6 or tif225 or ydr211w or yd8142.12 or yd8142b.03. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.243     R-free:   0.272
Authors: T.Boesen,G.R.Andersen,G.D.Pavitt
Key ref:
T.Boesen et al. (2004). Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue. J Biol Chem, 279, 10584-10592. PubMed id: 14681227 DOI: 10.1074/jbc.M311055200
14-May-03     Release date:   10-Feb-04    
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Protein chain
Pfam   ArchSchema ?
P32501  (EI2BE_YEAST) -  Translation initiation factor eIF-2B subunit epsilon
712 a.a.
161 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M311055200 J Biol Chem 279:10584-10592 (2004)
PubMed id: 14681227  
Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue.
T.Boesen, S.S.Mohammad, G.D.Pavitt, G.R.Andersen.
Eukaryotic initiation factor (eIF) 2B catalyzes the nucleotide activation of eIF2 to its active GTP-bound state. The exchange activity has been mapped to the C terminus of the eIF2Bepsilon subunit. We have determined the crystal structure of residues 544-704 from yeast eIF2Bepsilon at 2.3-A resolution, and this fragment is an all-helical protein built around the conserved aromatic acidic (AA) boxes also found in eIF4G and eIF5. The eight helices are organized in a manner similar to HEAT repeats. The molecule is highly asymmetric with respect to surface charge and conservation. One area in the N terminus is proposed to be directly involved in catalysis. In agreement with this hypothesis, mutation of glutamate 569 is shown to be lethal. An acidic belt and a second area in the C terminus containing residues from the AA boxes are important for binding to eIF2. Two mutations causing the fatal human genetic disease leukoencephalopathy with vanishing white matter are buried and appear to disrupt the structural integrity of the catalytic domain rather than interfering directly with catalysis or binding of eIF2.
  Selected figure(s)  
Figure 1.
FIG. 1. Electron density of helix VIII from the experimental map obtained from MAD phases after density modification. Helix VIII of one molecule of eIF2B C (gray carbons) packs with a symmetry related helix VIII (gold carbons). The contacts are dominated by the stacking of Trp699 with the corresponding residue of the neighbor molecule. The electron density map is contoured at 1.7 and plotted with the map_cover option in the program O (18) using a radius of 1 Å.
Figure 4.
FIG. 4. Stereoview of superimposition of C traces of eIF2B C (gray), eight helices of the human 80-kDa subunit of the cap binding complex (red), and six helices of the middle domain of human eIF4GII (blue). The C-terminal six helices of eIF2B C constitute a structural core in common with the 80-kDa subunit of the cap binding complex (27) and eIF4GII (28). Helix numbering is shown in Roman numerals.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 10584-10592) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19736320 C.H.Nguyen, H.Ming, P.Zhao, L.Hugendubler, R.Gros, S.R.Kimball, and P.Chidiac (2009).
Translational control by RGS2.
  J Cell Biol, 186, 755-765.  
18160716 X.Wang, and C.G.Proud (2008).
A novel mechanism for the control of translation initiation by amino acids, mediated by phosphorylation of eukaryotic initiation factor 2B.
  Mol Cell Biol, 28, 1429-1442.  
17526738 S.S.Mohammad-Qureshi, R.Haddad, E.J.Hemingway, J.P.Richardson, and G.D.Pavitt (2007).
Critical contacts between the eukaryotic initiation factor 2B (eIF2B) catalytic domain and both eIF2beta and -2gamma mediate guanine nucleotide exchange.
  Mol Cell Biol, 27, 5225-5234.  
16990799 C.R.Singh, B.Lee, T.Udagawa, S.S.Mohammad-Qureshi, Y.Yamamoto, G.D.Pavitt, and K.Asano (2006).
An eIF5/eIF2 complex antagonizes guanine nucleotide exchange by eIF2B during translation initiation.
  EMBO J, 25, 4537-4546.  
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.  
16153175 A.G.Hinnebusch (2005).
Translational regulation of GCN4 and the general amino acid control of yeast.
  Annu Rev Microbiol, 59, 407-450.  
15659334 C.G.Proud (2005).
eIF2 and the control of cell physiology.
  Semin Cell Dev Biol, 16, 3.  
15964804 C.R.Singh, C.Curtis, Y.Yamamoto, N.S.Hall, D.S.Kruse, H.He, E.M.Hannig, and K.Asano (2005).
Eukaryotic translation initiation factor 5 is critical for integrity of the scanning preinitiation complex and accurate control of GCN4 translation.
  Mol Cell Biol, 25, 5480-5491.  
16254050 Y.Yamamoto, C.R.Singh, A.Marintchev, N.S.Hall, E.M.Hannig, G.Wagner, and K.Asano (2005).
The eukaryotic initiation factor (eIF) 5 HEAT domain mediates multifactor assembly and scanning with distinct interfaces to eIF1, eIF2, eIF3, and eIF4G.
  Proc Natl Acad Sci U S A, 102, 16164-16169.  
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.