title: Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKaCalculations.
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 pKacalculation 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 pKadata 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 pKavalues 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.
authors.affiliation: Biochemistry-Electrochemistry Research Group and School of Chemistry, Institute of Science, Suranaree University of Technology , Nakhon Ratchasima 30000, Thailand.
authors.forename: Piyanat
authors.initials: P
authors.lastname: Meekrathok
authors.affiliation: School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland.
authors.forename: Predrag
authors.initials: P
authors.lastname: Kukic
authors.affiliation: School of Biomolecular and Biomedical Science, University College Dublin , Belfield, Dublin 4, Ireland.
authors.forename: Jens Erik
authors.initials: JE
authors.lastname: Nielsen
authors.affiliation: Biochemistry-Electrochemistry Research Group and School of Chemistry, Institute of Science, Suranaree University of Technology , Nakhon Ratchasima 30000, Thailand.|Centre of Excellence in Advanced Functional Materials, Suranaree University of Technology , Nakhon Ratchasima 30000, Thailand.
authors.forename: Wipa
authors.identifier: 0000-0001-5927-7192
authors.initials: W
authors.lastname: Suginta
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002688:Chitinases / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D016415:Sequence Alignment
chemical_list: D002688:Chitinases