The key structural determinant for recognition of HIF-1α by VHL is a hydroxyproline residue of the substrate that is hydroxylated under normoxic conditions in an oxygen-dependent manner [ 57].
The 3′-end of RydC has a U-rich tail that - together with a strong hairpin structure - facilitates Rho-independent transcription termination and which is an important determinant for recognition of many sRNAs (Otaka et al., 2011; Sauer and Weichenrieder, 2011; Ishikawa et al., 2012).
However such a mechanism could provide a solution to the problem of how diverse substrates are accepted if the CoA moiety is an important determinant for recognition and cleavage potentially enables separate permeation pathways for the polar (CoA) and hydrophobic (fatty acid) moieties of β-oxidation substrates.
We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of the adenine moiety of ATP by proteins.
These experiments also demonstrated the importance of the CH-C region as an anti-determinant for recognition of CA25 by the fungal GPI-T; truncated peptide substrates, wherein this region is deleted, are more active GPI-T substrates than the full-length CA25 peptide (R. Morissette, Y. Varma and T. Hendrickson, unpublished work).
Determinants for recognition of the histone code are being revealed by a growing body of experimental data providing valuable information on the molecular tractability of binding sites involved in epigenetic signalling [ 501], which will enhance further insight to epigenetic function.
Indeed, previous studies proposed that the acidic C-terminal region of Hsp104 acts as a substrate-binding determinant for prion recognition [7].
The majority of these mutations simply improve splice site strength, which is consistent with splice site strength being the major determinant for exon recognition.
Although there are no consensus sequences identified in palmitoylation substrates, a few determinants necessary for recognition by PATs have been described [25], [26].
Determinants important for recognition of TIR are located between positions -20 and +15 [ 1], including mRNA secondary structure, purine-rich Shine-Dalgarno region (SD) (AGGAGG in Escherichia coli) [ 2- 4], S1 protein binding A/U-rich enhancer [ 4- 6], spacing between SD and start codon [ 7, 8], the base immediately preceding the initiation codon [ 9] and the identity of the start codon [ 10].
The NBS domain, including ATPase and G proteins, plays an important role in the plant immune response through signal transduction, while the LRR domain, a major determinant of recognition specificity, is responsible for Avr gene recognition [ 39, 40].
