While it seems that active site dimension contributes to potassium specificity, inspection of the active site of YqeH model suggests that like in MnmE, potassium is bound at the active site by main chain interactions with a part of switch-I, termed the K-loop, α and β phosphates of GDP, a fluoride ion (i.e. the γ-phosphate mimic) and the side chain of Asn-169 from P-loop (Fig. 4a).
DOI: http://dx.doi.org/10.7554/eLife.07141.009 Closer inspection of the active site in the superposition (again, aligned by the active site finger loop) reveals that the movements described above directly affect substrate binding.
Unexpectedly, inspection of the active site region of DmPAO evidenced a stronger structural similarity with the SMOs active site than with that of the invertebrate PAO and of FMS1.
Inspection of the active site of both structures shows that upon ertapenem binding, there are only minor movements of the active site residues.
Inspection of the active site architecture suggested that the enantioselectivity derives from the local surface features that make intimate contact with the substrate diol.
Closer inspection of the active site of the DprE1-PBTZ169 structure (Fig 3B) shows that the benzothiazinone ring interacts with the same residues in the active site as previously observed in the M. smegmatis DprE1-BTZ043 structure.
Inspection of the active site of GLI does not reveal either a general base that would activate the 4-OH group of the δ-lactone for intramolecular attack on the lactone carbonyl group or a nucleophile that would allow the formation of an acyl enzyme intermediate that would partition between the δ- and γ-lactones.
In particular, there is no way to discern from structural inspection of an active site whether all neighbors have substantial energetic interactions, the scale and form of these energetic connections, or whether and how far beyond nearest neighbors functional effects extend.
At trimming chute inspections, prevalence of active DD lesions decreased from start to the end of the trial (22 and 14%, respectively); concurrently, prevalence of feet with no DD lesions (M0) increased (39 and 48%).
All annotations were confirmed by manual inspection, including confirmation of active residues and phylogenetic tree analyses.
