Journal Article


Wipa Suginta
Jens Erik Nielsen
Predrag Kukic
Piyanat Meekrathok



models molecular amino acid sequence hydrogen ion concentration metabolism chemical phenomena amino acid motifs chemistry chitinases sequence alignment databases protein

Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations. (2017)

Abstract GH-18 chitinases are chitinolytic enzymes, primarily responsible for the recycling of insoluble chitin biomaterials. These enzymes contain three invariant acidic active-site residues within a DXDXE motif, which play a synergistic role in the catalytic cycle of chitin degradation. We employed a pKa calculation approach to approximate the protonation states of residues D1, D2, and E in the DXDXE motif of 75 GH-18 chitinases. Theoretical pH-activity profiles of these enzymes were subsequently constructed and compared with the experimentally determined pH-activity profiles. Theoretical pKa data indicate that in the majority of chitinases the D1 side-chain is in the "up" and the E side-chain in the "down" position, while the position of the D2 side-chain is versatile and depends on the state of the enzyme. The pKa values in 75 GH-18 chitinases were predicted to be <0 for D1, 8-13 for D2, and 6-9 for E, indicating that the D1-D2 pair holds exactly one net negative charge. On the other hand, the catalytic acid E is protonated over the active pH-range, agreeing with the pH-activity curves reported previously for most chitinases. The results obtained from this study help to elucidate the mechanistic details of the concerted participation of D1, D2, and E in the catalytic cycle of chitin hydrolysis by GH-18 chitinases.
Collections Ireland -> University College Dublin -> PubMed

Full list of authors on original publication

Wipa Suginta, Jens Erik Nielsen, Predrag Kukic, Piyanat Meekrathok

Experts in our system

Jens Erik Nielsen
University College Dublin
Total Publications: 27