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PDBsum entry 1wb3
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protein ligands metals Protein-protein interface(s) links
Protein synthesis PDB id
1wb3

 

 

 

 

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Contents
Protein chains
451 a.a. *
381 a.a. *
346 a.a. *
Ligands
GNP ×2
SO4 ×6
DXC ×7
Metals
_MG ×2
* Residue conservation analysis
Superseded by: 4acb
PDB id:
1wb3
Name: Protein synthesis
Title: Crystal structure of translation elongation factor selb from methanococcus maripaludis in complex with the gtp analogue gppnhp
Structure: Translation elongation factor selb. Chain: a, b, c, d. Synonym: mj0495-like protein. Engineered: yes
Source: Methanococcus maripaludis. Organism_taxid: 39152. Strain: jj. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsm 2067)
Resolution:
3.20Å     R-factor:   0.347     R-free:   0.365
Authors: M.Leibundgut,C.Frick,M.Thanbichler,A.Boeck,N.Ban
Key ref:
M.Leibundgut et al. (2005). Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J, 24, 11-22. PubMed id: 15616587 DOI: 10.1038/sj.emboj.7600505
Date:
29-Oct-04     Release date:   04-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8J307  (Q8J307) -  SelB translation factor (Fragment) from Methanococcus maripaludis
Seq:
Struc: 		468 a.a.
451 a.a.*
Protein chain
Pfam   ArchSchema ?
Q8J307  (Q8J307) -  SelB translation factor (Fragment) from Methanococcus maripaludis
Seq:
Struc: 		468 a.a.
381 a.a.*
Protein chain
Pfam   ArchSchema ?
Q8J307  (Q8J307) -  SelB translation factor (Fragment) from Methanococcus maripaludis
Seq:
Struc: 		468 a.a.
346 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 

 
DOI no: 10.1038/sj.emboj.7600505 EMBO J 24:11-22 (2005)
PubMed id: 15616587  
 
 
Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors.
M.Leibundgut, C.Frick, M.Thanbichler, A.Böck, N.Ban.
 
  ABSTRACT  
 
In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5' phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a 'chalice' observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Overview of the SelB:GDP structure from M. maripaludis. (A) Structure of SelB molecule C in the GDP conformation. The C trace is rainbow coloured from the N- (blue) to the C-terminus (orange). SelB consists of four individual domains, denoted I, II, III and IV, which are arranged to form a 'molecular chalice'. The first three domains form the cup and the fourth the base of the chalice. The GDP nucleotide (red) is bound to domain I (blue), which carries the GTPase activity. (B) Flexibility of domain IV demonstrated by superposition of two different SelB:GDP molecules (chains A and C) in the asymmetric unit. The superposition of the first three domains shows that domain IV is flexibly linked to domain III. Its orientation in these two snapshots varies by an approximately 20° rotation. 		Figure 7.
Figure 7 Model of SelB bound to the GTPase activating centre of the 70S ribosome prior to the release of the tRNA. (A) Superposition of SelB domains I–III with the corresponding domains from the EF-Tu:GDP:Phe-tRNA^Phe:kirromycin complex bound to the 70S ribosome. After superposition of SelB (green) with EF-Tu (red), SelB domain IV points towards the mRNA entrance cleft of the small ribosomal subunit. The A/T state Phe-tRNA^Phe from the EF-Tu complex is depicted in blue. CP: central protuberance; L11: L11 region of the large subunit. (B) In the schematic representation, the crown view of the 50S subunit is shown (grey). Domain IV of SelB (green), which points towards the mRNA entrance cleft formed by the 30S subunit (yellow outline), would allow SelB to bind the SECIS element located in the 3' UTR of the mRNA (red) either directly or via an adapter protein. Sec-tRNA^Sec (blue) bound to SelB:GTP would recognize the internal UGA stop codon located in the A site of the small ribosomal subunit (shown as 'stop signal'). The usual UAA or UAG stop codon of the gene is indicated with a red dot, and the tRNAs located in the P and E sites are depicted in magenta and brown, respectively. L1: large ribosomal protein L1; CP: central protuberance; L11: L11 region of the large subunit.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 11-22) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082171 D.Caetano-Anollés, K.M.Kim, J.E.Mittenthal, and G.Caetano-Anollés (2011).
Proteome evolution and the metabolic origins of translation and cellular life.
  J Mol Evol, 72, 14-33.  
21265745 F.Blombach, S.J.Brouns, and J.van der Oost (2011).
Assembling the archaeal ribosome: roles for translation-factor-related GTPases.
  Biochem Soc Trans, 39, 45-50.  
21255425 G.C.Atkinson, V.Hauryliuk, and T.Tenson (2011).
An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea.
  BMC Evol Biol, 11, 22.  
21102444 A.M.van den Elzen, J.Henri, N.Lazar, M.E.Gas, D.Durand, F.Lacroute, M.Nicaise, H.van Tilbeurgh, B.Séraphin, and M.Graille (2010).
Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.
  Nat Struct Mol Biol, 17, 1446-1452.
PDB codes: 3p26 3p27
19940162 A.Paleskava, A.L.Konevega, and M.V.Rodnina (2010).
Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB.
  J Biol Chem, 285, 3014-3020.  
  20871851 B.de Koning, F.Blombach, S.J.Brouns, and J.van der Oost (2010).
Fidelity in archaeal information processing.
  Archaea, 2010, 0.  
19747061 J.Donovan, and P.R.Copeland (2010).
Threading the needle: getting selenocysteine into proteins.
  Antioxid Redox Signal, 12, 881-892.  
20623998 S.Palioura, J.Herkel, M.Simonović, A.W.Lohse, and D.Söll (2010).
Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.
  Biol Chem, 391, 771-776.  
19692584 Y.Itoh, S.Chiba, S.Sekine, and S.Yokoyama (2009).
Crystal structure of human selenocysteine tRNA.
  Nucleic Acids Res, 37, 6259-6268.
PDB code: 3a3a
18502805 V.Hauryliuk, S.Hansson, and M.Ehrenberg (2008).
Cofactor dependent conformational switching of GTPases.
  Biophys J, 95, 1704-1715.  
17901155 A.V.Beribisky, T.J.Tavares, A.N.Amborski, M.Motamed, A.E.Johnson, T.L.Mark, and P.E.Johnson (2007).
The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB.
  RNA, 13, 1948-1956.
PDB code: 2rlu
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.  
17456565 M.T.Howard, M.W.Moyle, G.Aggarwal, B.A.Carlson, and C.B.Anderson (2007).
A recoding element that stimulates decoding of UGA codons by Sec tRNA[Ser]Sec.
  RNA, 13, 912-920.  
17937620 N.Fischer, A.Paleskava, K.B.Gromadski, A.L.Konevega, M.C.Wahl, H.Stark, and M.V.Rodnina (2007).
Towards understanding selenocysteine incorporation into bacterial proteins.
  Biol Chem, 388, 1061-1067.  
17881825 O.Ganichkin, and M.C.Wahl (2007).
Conformational switches in winged-helix domains 1 and 2 of bacterial translation elongation factor SelB.
  Acta Crystallogr D Biol Crystallogr, 63, 1075-1081.
PDB code: 2v9v
17533454 T.Cathopoulis, P.Chuawong, and T.L.Hendrickson (2007).
Novel tRNA aminoacylation mechanisms.
  Mol Biosyst, 3, 408-418.  
17214893 T.Margus, M.Remm, and T.Tenson (2007).
Phylogenetic distribution of translational GTPases in bacteria.
  BMC Genomics, 8, 15.  
17502103 T.Ose, N.Soler, L.Rasubala, K.Kuroki, D.Kohda, D.Fourmy, S.Yoshizawa, and K.Maenaka (2007).
Structural basis for dynamic interdomain movement and RNA recognition of the selenocysteine-specific elongation factor SelB.
  Structure, 15, 577-586.
PDB code: 2uwm
  16754981 C.Förster, N.Krauss, A.B.Brauer, K.Szkaradkiewicz, S.Brode, K.Hennig, J.P.Fürste, M.Perbandt, C.Betzel, and V.A.Erdmann (2006).
Crystallization and preliminary X-ray diffraction analysis of a tRNASer acceptor-stem microhelix.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 559-561.  
16478999 L.A.de Jesus, P.R.Hoffmann, T.Michaud, E.P.Forry, A.Small-Howard, R.J.Stillwell, N.Morozova, J.W.Harney, and M.J.Berry (2006).
Nuclear assembly of UGA decoding complexes on selenoprotein mRNAs: a mechanism for eluding nonsense-mediated decay?
  Mol Cell Biol, 26, 1795-1805.  
15863725 D.Su, Y.Li, and V.N.Gladyshev (2005).
Selenocysteine insertion directed by the 3'-UTR SECIS element in Escherichia coli.
  Nucleic Acids Res, 33, 2486-2492.  
15870727 M.J.Berry (2005).
Knowing when not to stop.
  Nat Struct Mol Biol, 12, 389-390.  
15791204 M.T.Howard, G.Aggarwal, C.B.Anderson, S.Khatri, K.M.Flanigan, and J.F.Atkins (2005).
Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons.
  EMBO J, 24, 1596-1607.  
16113240 T.Suematsu, A.Sato, M.Sakurai, K.Watanabe, and T.Ohtsuki (2005).
A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2.
  Nucleic Acids Res, 33, 4683-4691.  
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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