Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 90, Issue 1, Pages 123-130Publisher
WILEY
DOI: 10.1002/prot.26191
Keywords
2-pyrone-4; 6-dicarboxylate lactonase; EVB; histidine protonation state; lactonase; LigI reaction mechanism
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Funding
- Agency for Science, Technology and Research (A*STAR) International Fellowship (AIF)
- IngaBritt och Arne Lundbergs Forskningsstiftelse [LU2020-0013]
- Crafoord Foundation
- Faculty of Medicine, Lund University
- Swedish Foundation for Strategic Research [IRC15-0067]
- Swedish Research Council, Strategic Research Area EXODIAB [Dnr 2009 1039]
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Research has shown that changes in pH can affect the catalytic activity of lignin-degrading enzymes, highlighting the determinant role of protonation state of active site residues in the hydrolysis of PDC.
Lignin is one of the world's most abundant organic polymers, and 2-pyrone-4,6-dicarboxylate lactonase (LigI) catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) in the degradation of lignin. The pH has profound effects on enzyme catalysis and therefore we studied this in the context of LigI. We found that changes of the pH mostly affects surface residues, while the residues at the active site are more subject to changes of the surrounding microenvironment. In accordance with this, a high pH facilitates the deprotonation of the substrate. Detailed free energy calculations by the empirical valence bond (EVB) approach revealed that the overall hydrolysis reaction is more likely when the three active site histidines (His31, His33 and His180) are protonated at the e site, however, protonation at the delta site may be favored during specific steps of the reaction. Our studies have uncovered the determinant role of the protonation state of the active site residues His31, His33 and His180 in the hydrolysis of PDC.
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