PDBsum entry 2ply

Translation/RNA

PDB id: 2ply

Contents

Protein chains

212 a.a. *

198 a.a. *

DNA/RNA

Metals

_NA

_MG ×17

_CL ×4

_CA ×2

Waters ×109

* Residue conservation analysis

PDB id:

2ply

Name:

Translation/RNA

Title:

Structure of the mRNA binding fragment of elongation factor selb in complex with secis RNA.

Structure:

RNA (5'- r( Gp Gp Cp Gp Up Up Gp Cp Cp Gp Gp Up Cp Up Gp Gp Cp Ap Ap Cp Gp Cp C)-3'). Chain: c, e. Engineered: yes. Other_details: secis RNA. Selenocysteine-specific elongation factor. Chain: a, b. Synonym: selb translation factor.

Source:

Synthetic: yes. Other_details: in vitro transcription. Moorella thermoacetica. Organism_taxid: 1525. Gene: selb. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.230 R-free: 0.287

Authors:

N.Soler,D.Fourmy,S.Yoshizawa

Key ref:

N.Soler et al. (2007). Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB. J Mol Biol, 370, 728-741. PubMed id: 17537456 DOI: 10.1016/j.jmb.2007.05.001

Date:

20-Apr-07 Release date: 06-Nov-07

Protein chain

Q46455  (SELB_MOOTH) -  Selenocysteine-specific elongation factor from Moorella thermoacetica

Seq: 634 a.a.

Struc: 212 a.a.*

Protein chain

Q46455  (SELB_MOOTH) -  Selenocysteine-specific elongation factor from Moorella thermoacetica

Seq: 634 a.a.

Struc: 198 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

DNA/RNA chains

G-G-C-G-U-U-G-C-C-G-G-U-C-U-G-G-C-A-A-C-G-C-C 23 bases

G-G-C-G-U-U-G-C-C-G-G-U-C-U-G-G-C-A-A-C-G-C-C 23 bases

DOI no: 10.1016/j.jmb.2007.05.001

J Mol Biol 370:728-741 (2007)

PubMed id: 17537456

Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB.

N.Soler, D.Fourmy, S.Yoshizawa.

ABSTRACT

Elongation factor SelB is responsible for co-translational incorporation of selenocysteine (Sec) into proteins. The UGA stop codon is recoded as a Sec codon in the presence of a downstream mRNA hairpin. In prokaryotes, in addition to the EF-Tu-like N-terminal domains, a C-terminal extension containing four tandem winged-helix motifs (WH1-4) recognizes the mRNA hairpin. The 2.3-A resolution crystal structure of the Escherichia coli WH3/4 domains bound to mRNA with mutagenesis data reveal that the two WH motifs use the same structural elements to bind RNA. The structure together with the 2.6-A resolution structure of the WH1-4 domains from Moorella thermoacetica bound to RNA revealed that a salt bridge connecting WH2 to WH3 modules is disrupted upon mRNA binding. The results provide a structural basis for the molecular switch that may allow communication between tRNA and mRNA binding sites and illustrate how RNA acts as an activator of the switch. The structures show that tandem WH motifs not only provide an excellent scaffold for RNA binding but can also have an active role in the function of protein-RNA complexes.

Selected figure(s)

Figure 1.

Figure 6.
Figure 6. Comparison of protein–RNA interactions in the SelB WH–RNA complexes with other nucleic acid–WH complexes. The WH motifs are in the same orientation. (a) Protein–RNA recognition in the E. coli WH4–SECIS RNA complex. The N-terminal regions of helices H2 and H3 and β strands that interact with the RNA hairpin are in red. (b) Protein–RNA recognition in crystal contacts within the M. thermoacetica WH2–SECIS RNA complex. The connecting loop between helix H1 and strand S1 is in red. (c) Protein–RNA recognition in crystal contacts within the M. thermoacetica WH3–SECIS RNA complex. The helix H3 is colored red. (d) Protein–RNA recognition in the La NTD–RNA complex (PDB code 1ZH5). Only the WH La motif is shown. The UUU[OH]3′ end segment is targeted by the C-terminal region of helix H1 and insertion helices H2 and H4 (in red). (e) The recognition helix of the WH motif in the Sap-1 protein–DNA complex (PDB code 1bc8,^54) is in red.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 728-741) copyright 2007.

Figures were selected by an automated process.