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PDBsum entry 1lva

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protein ligands metals links
Translation PDB id
1lva
Jmol
Contents
Protein chain
258 a.a. *
Ligands
SO4
Metals
_Y1 ×2
Waters ×108
* Residue conservation analysis
PDB id:
1lva
Name: Translation
Title: Crystal structure of a c-terminal fragment of moorella thermoacetica elongation factor selb
Structure: Selenocysteine-specific elongation factor. Chain: a. Fragment: c-terminal fragment. Synonym: selb translation factor, selb. Engineered: yes
Source: Moorella thermoacetica. Organism_taxid: 1525. Gene: selb(amino acids 370-634). Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.12Å     R-factor:   0.215     R-free:   0.258
Authors: M.Selmer,X.-D.Su
Key ref:
M.Selmer and X.D.Su (2002). Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. EMBO J, 21, 4145-4153. PubMed id: 12145214 DOI: 10.1093/emboj/cdf408
Date:
28-May-02     Release date:   21-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q46455  (SELB_MOOTH) -  Selenocysteine-specific elongation factor
Seq:
Struc:
 
Seq:
Struc:
634 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     selenocysteine incorporation   1 term 
  Biochemical function     RNA binding     3 terms  

 

 
DOI no: 10.1093/emboj/cdf408 EMBO J 21:4145-4153 (2002)
PubMed id: 12145214  
 
 
Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
M.Selmer, X.D.Su.
 
  ABSTRACT  
 
SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). We present the crystal structure of a C-terminal fragment of SelB (SelB-C) from Moorella thermoacetica at 2.12 A resolution, solved by a combination of selenium and yttrium multiwavelength anomalous dispersion. This 264 amino acid fragment contains the entire C-terminal extension beginning after the EF-Tu-homologous domains. SelB-C consists of four similar winged-helix domains arranged into the shape of an L. This is the first example of winged-helix domains involved in RNA binding. The location of conserved basic amino acids, together with data from the literature, define the position of the mRNA-binding site. Steric requirements indicate that a conformational change may occur upon ribosome interaction. Structural observations and data in the literature suggest that this change happens upon mRNA binding.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Section of the final 2F[o] - F[c] map showing the coordination of the sulfate ion by Arg599, Ser605 and Arg606, prepared using O (Jones et al., 1991).
Figure 7.
Figure 7 Canonical binding of double-stranded DNA to a winged-helix domain in the structure of Sap1 bound to the E74 promoter (Protein Data Bank code 1bc8; Mo et al., 1998). The image was prepared using Rasmol (Bernstein, 2000).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 4145-4153) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
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
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.  
  17565186 N.Soler, D.Fourmy, and S.Yoshizawa (2007).
Crystallization and preliminary X-ray analysis of the mRNA-binding domain of elongation factor SelB from Escherichia coli in complex with RNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 419-421.  
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
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
16387655 M.Teplova, Y.R.Yuan, A.T.Phan, L.Malinina, S.Ilin, A.Teplov, and D.J.Patel (2006).
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.
  Mol Cell, 21, 75-85.
PDB codes: 1yty 1zh5
16648637 S.Caputo, J.Couprie, I.Duband-Goulet, E.Kondé, F.Lin, S.Braud, M.Gondry, B.Gilquin, H.J.Worman, and S.Zinn-Justin (2006).
The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain.
  J Biol Chem, 281, 18208-18215.
PDB code: 2ch0
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
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 4ac9 4aca 4acb
15665870 S.Yoshizawa, L.Rasubala, T.Ose, D.Kohda, D.Fourmy, and K.Maenaka (2005).
Structural basis for mRNA recognition by elongation factor SelB.
  Nat Struct Mol Biol, 12, 198-203.
PDB code: 1wsu
14976553 G.Dong, G.Chakshusmathi, S.L.Wolin, and K.M.Reinisch (2004).
Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch.
  EMBO J, 23, 1000-1007.
PDB code: 1s29
15704013 W.A.McLaughlin, D.W.Kulp, J.de la Cruz, X.J.Lu, C.L.Lawson, and H.M.Berman (2004).
A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
  J Struct Funct Genomics, 5, 255-265.  
15180986 Z.Wei, P.Zhang, Z.Zhou, Z.Cheng, M.Wan, and W.Gong (2004).
Crystal structure of human eIF3k, the first structure of eIF3 subunits.
  J Biol Chem, 279, 34983-34990.
PDB code: 1rz4
12351842 M.Selmer, R.Wilting, D.Holmlund, and X.D.Su (2002).
Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
  Acta Crystallogr D Biol Crystallogr, 58, 1871-1873.  
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.