X-Ray Analysis of Prokaryotic and Eukaryotic Ribosomes - Biophysical Approaches to Translational Control of Gene Expression - page 4

Shine-Dalgarno (SD) sequence, UUU (Phe) codons in the A and P sites, and
tRNA Phe . The structure of this complex was determined at 3.1 Å resolution. Crystals
of the ribosome complex modeling the initiation state were prepared with a 27
nucleotide long mRNA comprising the SD sequence with AUG (Met) codon and
initiator tRNA fMet in the P site. The structure of this complex was determined at
3.5 Å resolution.

1.2.2 A Novel Intersubunit Bridge Formed by Protein L31 May

Regulate Swiveling of the 30S Head

Inspection of the electron density map corresponding to our elongation state revealed
well-defined density for a novel element not fully seen in previous high-resolution
structures. This element was the ribosomal protein L31 (Figs. 1.1 and 1.2 ) (Jenner
et al. 2010a, b ) .
Protein L31 displays a considerable degree of similarity among bacteria
(Fig. 1.2a ), and is comprised of a three b-sheets Zn-binding domain followed by a
loop area and an a-helix at its C-terminal. Interestingly, L31 crosses the intersubunit
space yoking together the central protuberance of the 50S subunit and the head
domain of the 30S subunit. At the 30S subunit head, L31 interacts with the two
highly conserved proteins S13 and S19 that are known to form a loose hetero-dimer
(Brodersen et al. 2002 ) (Fig. 1.2b ).
Protein S13 is part of the B1a and B1b intersubunit bridges and has a C-terminal
that approaches the P site (Yusupov et al. 2001 ) . The central part of L31 (amino
acids 32-52) interacts directly with S13 mostly through electrostatic interactions
(Fig. 1.2c ) while the interaction surface between S19 and L31 is not only of polar
but also hydrophobic nature (Fig. 1.2d ). The majority of the interacting residues of
proteins S13, S19, and L31 are conserved. Overall, protein L31 clips together the
globular N-domains of S13 and S19, presumably tightening their association.
The biological relevance of this intersubunit bridge composed of protein L31
may lie in regulating and safeguarding the swiveling of the 30S subunit head domain.
It might function as a safety belt, delimiting the extent of 30S head rotation, in the
ratchet-like motion supposed to happen during translocation (Spahn et al. 2004a ;
Frank and Agrawal 2000 ; Gao et al. 2003 ) .

1.2.3 The Path of Messenger RNA Through the Ribosome

In the initial high-resolution (2.8-3.6 Å) structures of 70S ribosomal complexes, the
mRNA was visualized only from positions −4 to +7 (Selmer et al. 2006 ; Weixlbaumer
et al. 2007a, b ; Korostelev et al. 2008 ; Laurberg et al. 2008 ) although earlier medium
resolution structures (4.5-5.5 Å) had previously indicated the entire mRNA path
(Jenner et al. 2007, 2005 ; Yusupova et al. 2006, 2001 ). In our recent high-resolution