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PDBsum entry 2vsx
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protein ligands Protein-protein interface(s) links
Translation/hydrolase PDB id
2vsx

 

 

 

 

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Contents
Protein chains
366 a.a. *
240 a.a. *
Ligands
AMP ×2
* Residue conservation analysis
PDB id:
2vsx
Name: Translation/hydrolase
Title: Crystal structure of a translation initiation complex
Structure: Atp-dependent RNA helicase eif4a. Chain: a, b. Synonym: eukaryotic initiation factor 4a, eif-4a, translation initiation factor 1/2, stimulator factor i 37 kda component, p37eif4a. Engineered: yes. Eukaryotic initiation factor 4f subunit p150. Chain: e, f. Fragment: middle domain, 4a-binding, residues 572-854.
Source: Saccharomyces cerevisiae. Organism_taxid: 4932. Atcc: 96604. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: rosetta. Expression_system_taxid: 469008.
Resolution:
2.80Å     R-factor:   0.254     R-free:   0.287
Authors: P.Schutz,M.Bumann,A.E.Oberholzer,C.Bieniossek,M.Altmann,H.Trachsel, U.Baumann
Key ref: P.Schütz et al. (2008). Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions. Proc Natl Acad Sci U S A, 105, 9564-9569. PubMed id: 18606994
Date:
30-Apr-08     Release date:   24-Jun-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10081  (IF4A_YEAST) -  ATP-dependent RNA helicase eIF4A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		395 a.a.
366 a.a.
Protein chains
Pfam   ArchSchema ?
P39935  (IF4F1_YEAST) -  Eukaryotic initiation factor 4F subunit p150 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		952 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 =
ADP
Bound ligand (Het Group name = AMP)
matches with 85.19% similarity 		+ phosphate
 + H(+)
   Enzyme class 2: Chains E, F: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 105:9564-9569 (2008)
PubMed id: 18606994  
 
 
Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions.
P.Schütz, M.Bumann, A.E.Oberholzer, C.Bieniossek, H.Trachsel, M.Altmann, U.Baumann.
 
  ABSTRACT  
 
Translation initiation factors eIF4A and eIF4G form, together with the cap-binding factor eIF4E, the eIF4F complex, which is crucial for recruiting the small ribosomal subunit to the mRNA 5' end and for subsequent scanning and searching for the start codon. eIF4A is an ATP-dependent RNA helicase whose activity is stimulated by binding to eIF4G. We report here the structure of the complex formed by yeast eIF4G's middle domain and full-length eIF4A at 2.6-A resolution. eIF4A shows an extended conformation where eIF4G holds its crucial DEAD-box sequence motifs in a productive conformation, thus explaining the stimulation of eIF4A's activity. A hitherto undescribed interaction involves the amino acid Trp-579 of eIF4G. Mutation to alanine results in decreased binding to eIF4A and a temperature-sensitive phenotype of yeast cells that carry a Trp579Ala mutation as its sole source for eIF4G. Conformational changes between eIF4A's closed and open state provide a model for its RNA-helicase activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23340841 H.Firczuk, S.Kannambath, J.Pahle, A.Claydon, R.Beynon, J.Duncan, H.Westerhoff, P.Mendes, and J.E.McCarthy (2013).
An in vivo control map for the eukaryotic mRNA translation machinery.
  Mol Syst Biol, 9, 635.  
21441902 B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, and K.Weis (2011).
A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.
  Nature, 472, 238-242.
PDB codes: 3peu 3pev 3pew 3pex 3pey 3pez 3rrm 3rrn
21428949 D.Klostermeier (2011).
Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling.
  Biochem Soc Trans, 39, 611-616.  
21113134 I.S.Abaeva, A.Marintchev, V.P.Pisareva, C.U.Hellen, and T.V.Pestova (2011).
Bypassing of stems versus linear base-by-base inspection of mammalian mRNAs during ribosomal scanning.
  EMBO J, 30, 115-129.  
21391900 J.Strohmeier, I.Hertel, U.Diederichsen, M.G.Rudolph, and D.Klostermeier (2011).
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
  Biol Chem, 392, 357-369.
PDB codes: 3mwj 3mwk 3mwl 3nbf 3nej
21113024 K.H.Nielsen, M.A.Behrens, Y.He, C.L.Oliveira, L.S.Jensen, S.V.Hoffmann, J.S.Pedersen, and G.R.Andersen (2011).
Synergistic activation of eIF4A by eIF4B and eIF4G.
  Nucleic Acids Res, 39, 2678-2689.  
21062831 M.Hilbert, F.Kebbel, A.Gubaev, and D.Klostermeier (2011).
eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism.
  Nucleic Acids Res, 39, 2260-2270.  
21437710 V.López-Ramírez, L.D.Alcaraz, G.Moreno-Hagelsieb, and G.Olmedo-Álvarez (2011).
Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins.
  J Mol Evol, 72, 413-431.  
20694742 A.D.Lellis, M.L.Allen, A.W.Aertker, J.K.Tran, D.M.Hillis, C.R.Harbin, C.Caldwell, D.R.Gallie, and K.S.Browning (2010).
Deletion of the eIFiso4G subunit of the Arabidopsis eIFiso4F translation initiation complex impairs health and viability.
  Plant Mol Biol, 74, 249-263.  
  20229607 E.Bae, E.Bitto, C.A.Bingman, J.G.McCoy, G.E.Wesenberg, and G.N.Phillips (2010).
Crystal structure of an eIF4G-like protein from Danio rerio.
  Proteins, 78, 1803-1806.
PDB code: 2i2o
20479275 G.Buchwald, J.Ebert, C.Basquin, J.Sauliere, U.Jayachandran, F.Bono, H.Le Hir, and E.Conti (2010).
Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.
  Proc Natl Acad Sci U S A, 107, 10050-10055.
PDB code: 2xb2
20094052 R.J.Jackson, C.U.Hellen, and T.V.Pestova (2010).
The mechanism of eukaryotic translation initiation and principles of its regulation.
  Nat Rev Mol Cell Biol, 11, 113-127.  
20711189 S.N.Floor, B.N.Jones, G.A.Hernandez, and J.D.Gross (2010).
A split active site couples cap recognition by Dcp2 to activation.
  Nat Struct Mol Biol, 17, 1096-1101.  
19203580 A.Marintchev, K.A.Edmonds, B.Marintcheva, E.Hendrickson, M.Oberer, C.Suzuki, B.Herdy, N.Sonenberg, and G.Wagner (2009).
Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation.
  Cell, 136, 447-460.  
19299142 G.Hernández (2009).
On the origin of the cap-dependent initiation of translation in eukaryotes.
  Trends Biochem Sci, 34, 166-175.  
19204291 J.H.Chang, Y.H.Cho, S.Y.Sohn, J.M.Choi, A.Kim, Y.C.Kim, S.K.Jang, and Y.Cho (2009).
Crystal structure of the eIF4A-PDCD4 complex.
  Proc Natl Acad Sci U S A, 106, 3148-3153.
PDB code: 2zu6
19748356 M.Del Campo, and A.M.Lambowitz (2009).
Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.
  Mol Cell, 35, 598-609.
PDB codes: 3i5x 3i5y 3i61 3i62
19747077 M.Hilbert, A.R.Karow, and D.Klostermeier (2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.
  Biol Chem, 390, 1237-1250.  
19239892 N.Sonenberg, and A.G.Hinnebusch (2009).
Regulation of translation initiation in eukaryotes: mechanisms and biological targets.
  Cell, 136, 731-745.  
19153607 P.G.Loh, H.S.Yang, M.A.Walsh, Q.Wang, X.Wang, Z.Cheng, D.Liu, and H.Song (2009).
Structural basis for translational inhibition by the tumour suppressor Pdcd4.
  EMBO J, 28, 274-285.
PDB codes: 3eij 3eiq
19244245 R.Collins, T.Karlberg, L.Lehtiö, P.Schütz, S.van den Berg, L.G.Dahlgren, M.Hammarström, J.Weigelt, and H.Schüler (2009).
The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.
  J Biol Chem, 284, 10296-10300.
PDB codes: 3ews 3g0h
19470518 Y.Fujita, M.Oe, T.Tutsumino, S.Morino, H.Imataka, K.Tomoo, and T.Ishida (2009).
Domain-dependent interaction of eukaryotic initiation factor eIF4A for binding to middle and C-terminal domains of eIF4G.
  J Biochem, 146, 359-368.  
19805289 Z.Y.Dossani, C.S.Weirich, J.P.Erzberger, J.M.Berger, and K.Weis (2009).
Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1.
  Proc Natl Acad Sci U S A, 106, 16251-16256.
PDB code: 3gfp
18971945 M.A.Mir, and A.T.Panganiban (2008).
A protein that replaces the entire cellular eIF4F complex.
  EMBO J, 27, 3129-3139.  
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 codes are shown on the right.

 

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