This site, located at the 5' untranslated region (UTR)
of the mRNA transcript, regulates protein synthesis based on its sequence
and structure. There are two consensus sequences, named Kozak and Shine
Dalgarno (after their discoverers), which are known
to facilitate efficient translation in Eukaryotes and Prokaryotes respectively.
chart for more details.
||Preferred sequence context which allows effective ribosomal
binding at initiation site. The favored context is:
-6 -5 -4 -3 -2 -1 1 2 3 4
G C C A C C A U G G
around the initiating methionine (AUG), with the A at the -3 being the most important, and a purine at +4, preferably G being next most influential. [Kozak, M. (1991) J. Biol. Chem. 266, 19867-19870.(pdf)
||The SD sequence is complementary to the 3' end of the
16S rRNA. Its consensus sequence is 5'-UAAGGAGG-3' which is followed by
an initiation codon, most commonly AUG.
(About 8% of start sites use GUG, whereas UUG and AUU are rare initiators
present in autogenously regulated genes). The optimal
spacing between the SD sequence and the start codon is 8 nt, but translation
initiation is severely affected only if this distance is reduced below
4 nt or increased above 14 nt. [Shine, J. and Dalgarno, L.
(1975) Eur. J. Biochem. 57, 221.]
An additional mRNA feature affecting translation initiation is the downstream box (DB), located after the initiation codon and complementary to bases 1469-1483 of the 16S rRNA. DBs consensus sequence is: 5'-AUGAAUCACAAAGUG-3'.
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