It is important to note that the results show how well certain peptides displace β-Ala-Lys-AMCA, and therefore do not demonstrate if the tested di- or tripeptides are actual substrates of YjdL.
Discussion
To date, several different POTs from bacteria, fungi, plants, and mammals have been characterized. The general consensus from the analyses is that these transporters are able to translocate di- and tripeptides albeit with differing affinities depending on the nature and position of the amino Obatoclax residues (reviewed by Daniel et al. [14]). Also, a peptide backbone does not seem to be a strict requirement for translocation [15].
We subsequently extended the most potent dipeptides, Tyr-Ala and Ala-Lys, with an alanyl residue (Table 1). However, the affinity for these tripeptides at YjdL decreased significantly upon elongation with an alanyl residue on either side (8 to >50 mM). This suggests that tripeptides are accommodated poorly in the active site of YjdL, a feature quite different from its homologs from E. coli. Of note, DppA from E. coli has also been shown to have a significantly higher specificity towards dipeptides (excluding Gly-Gly) [19]. Although this apparently seems similar to YjdL, there are major differences: YjdL binds Ala-Ala with very low affinity and binding increases dramatically upon specific changes of residues, whereas DppA binds Ala-Ala with high affinity and the nature of the residues (except Gly) effects the affinity to a lesser extent.
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Such low level of genetic differentiation
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