Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States; Tetrad Graduate Program, University of California, San Francisco, San Francisco, United States
Andrew K Ecker
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
Galen J Correy
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
Pooja Asthana
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
Iris D Young
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
Bryan Faust
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; Biophysics Graduate Program, University of California, San Francisco, San Francisco, United States
Michael C Thompson
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States; Department of Chemistry and Chemical Biology, University of California, Merced, Merced, United States
Ian B Seiple
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
Steven Van Dyken
Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, United States
Richard M Locksley
Department of Medicine, University of California, San Francisco, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States; University of California, Howard Hughes Medical Institute, San Francisco, San Francisco, United States
Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.
