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Gene regulation PDB id
1d1n
Jmol
Contents
Protein chain
99 a.a. *
* Residue conservation analysis
PDB id:
1d1n
Name: Gene regulation
Title: Solution structure of the fmet-trnafmet binding domain of becillus stearothermophillus translation initiation factor if2
Structure: Initiation factor 2. Chain: a. Fragment: c2 terminal domain. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: S.Meunier,S.Spurio,M.Czisch,R.Wechselberger,M.Gueunneugues
Key ref:
S.Meunier et al. (2000). Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2. EMBO J, 19, 1918-1926. PubMed id: 10775275 DOI: 10.1093/emboj/19.8.1918
Date:
20-Sep-99     Release date:   20-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04766  (IF2_GEOSE) -  Translation initiation factor IF-2
Seq:
Struc: 		 
Seq:
Struc: 		741 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     translational initiation   1 term 
  Biochemical function     translation initiation factor activity     2 terms  

 

 
DOI no: 10.1093/emboj/19.8.1918 EMBO J 19:1918-1926 (2000)
PubMed id: 10775275  
 
 
Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2.
S.Meunier, R.Spurio, M.Czisch, R.Wechselberger, M.Guenneugues, C.O.Gualerzi, R.Boelens.
 
  ABSTRACT  
 
The three-dimensional structure of the fMet-tRNA(fMet) -binding domain of translation initiation factor IF2 from Bacillus stearothermophilus has been determined by heteronuclear NMR spectroscopy. Its structure consists of six antiparallel beta-strands, connected via loops, and forms a closed beta-barrel similar to domain II of elongation factors EF-Tu and EF-G, despite low sequence homology. Two structures of the ternary complexes of the EF-Tu small middle dotaminoacyl-tRNA small middle dot GDP analogue have been reported and were used to propose and discuss the possible fMet-tRNA(fMet)-binding site of IF2.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Overall organization of the antiparallel -strands of IF2 C-2. The arrows indicate the -strands that are numbered. The start and end of each strand is indicated. Strand -1 starts with a -bulge (residues 647 and 648). 		Figure 5.
Figure 5 Structural homology between IF2 C-2 and the elongation factors EF-Tu and EF-G. Ribbon representations of the C[ ]traces of: (A) domain II of T.aquaticus EF-Tu (Nissen et al., 1995); (B) B.stearothermophilus IF2 C-2; and (C) domain II of T.thermophilus EF-G (Ævarsson et al., 1994). The N- and C-termini are indicated in each structure.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1918-1926) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21368145 A.S.Yassin, M.E.Haque, P.P.Datta, K.Elmore, N.K.Banavali, L.L.Spremulli, and R.K.Agrawal (2011).
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
  Proc Natl Acad Sci U S A, 108, 3918-3923.
PDB codes: 3izy 3izz
18945684 A.Sacan, I.H.Toroslu, and H.Ferhatosmanoglu (2008).
Integrated search and alignment of protein structures.
  Bioinformatics, 24, 2872-2879.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
15731104 F.Charrière, T.H.Tan, and A.Schneider (2005).
Mitochondrial initiation factor 2 of Trypanosoma brucei binds imported formylated elongator-type tRNA(Met).
  J Biol Chem, 280, 15659-15665.  
16081655 H.Wienk, S.Tomaselli, C.Bernard, R.Spurio, D.Picone, C.O.Gualerzi, and R.Boelens (2005).
Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2.
  Protein Sci, 14, 2461-2468.
PDB code: 1z9b
15616587 M.Leibundgut, C.Frick, M.Thanbichler, A.Böck, and N.Ban (2005).
Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors.
  EMBO J, 24, 11-22.
PDB codes: 1wb1 1wb2 1wb3
15477394 A.C.Spencer, and L.L.Spremulli (2004).
Interaction of mitochondrial initiation factor 2 with mitochondrial fMet-tRNA.
  Nucleic Acids Res, 32, 5464-5470.  
15385567 M.Steiner-Mosonyi, C.Creuzenet, R.A.Keates, B.R.Strub, and D.Mangroo (2004).
The Pseudomonas aeruginosa initiation factor IF-2 is responsible for formylation-independent protein initiation in P. aeruginosa.
  J Biol Chem, 279, 52262-52269.  
12569173 A.Marintchev, V.G.Kolupaeva, T.V.Pestova, and G.Wagner (2003).
Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners.
  Proc Natl Acad Sci U S A, 100, 1535-1540.  
12799364 A.S.Tibbetts, L.Oesterlin, S.Y.Chan, G.Kramer, B.Hardesty, and D.R.Appling (2003).
Mammalian mitochondrial initiation factor 2 supports yeast mitochondrial translation without formylated initiator tRNA.
  J Biol Chem, 278, 31774-31780.  
12600987 B.S.Laursen, K.K.Mortensen, H.U.Sperling-Petersen, and D.W.Hoffman (2003).
A conserved structural motif at the N terminus of bacterial translation initiation factor IF2.
  J Biol Chem, 278, 16320-16328.
PDB code: 1nd9
14622001 D.J.Sidote, and D.W.Hoffman (2003).
NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.
  Biochemistry, 42, 13541-13550.
PDB code: 1pc0
12581660 N.Sonenberg, and T.E.Dever (2003).
Eukaryotic translation initiation factors and regulators.
  Curr Opin Struct Biol, 13, 56-63.  
12869707 S.Marzi, W.Knight, L.Brandi, E.Caserta, N.Soboleva, W.E.Hill, C.O.Gualerzi, and J.S.Lodmell (2003).
Ribosomal localization of translation initiation factor IF2.
  RNA, 9, 958-969.  
11927568 G.Dong, J.Nowakowski, and D.W.Hoffman (2002).
Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.
  EMBO J, 21, 1845-1854.
PDB code: 1k8h
12056898 S.T.Hsu, E.Breukink, B.de Kruijff, R.Kaptein, A.M.Bonvin, and N.A.van Nuland (2002).
Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles.
  Biochemistry, 41, 7670-7676.  
11497435 A.La Teana, C.O.Gualerzi, and A.E.Dahlberg (2001).
Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA.
  RNA, 7, 1173-1179.  
11738593 A.Roll-Mecak, B.S.Shin, T.E.Dever, and S.K.Burley (2001).
Engaging the ribosome: universal IFs of translation.
  Trends Biochem Sci, 26, 705-709.  
12762039 C.O.Gualerzi, L.Brandi, E.Caserta, C.Garofalo, M.Lammi, A.La Teana, D.Petrelli, R.Spurio, J.Tomsic, and C.L.Pon (2001).
Initiation factors in the early events of mRNA translation in bacteria.
  Cold Spring Harb Symp Quant Biol, 66, 363-376.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
11714910 W.Li, and D.W.Hoffman (2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
  Protein Sci, 10, 2426-2438.
PDB code: 1jt8
11013225 M.Guenneugues, E.Caserta, L.Brandi, R.Spurio, S.Meunier, C.L.Pon, R.Boelens, and C.O.Gualerzi (2000).
Mapping the fMet-tRNA(f)(Met) binding site of initiation factor IF2.
  EMBO J, 19, 5233-5240.  
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.