Journal Article

IMPULSE-2021-00273

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid–Base Catalysis

Wan, Q. (Corresponding author) ; Bennett, B. C. ; Wymore, T. ; Li, Z. ; Wilson, M. A. ; Brooks, C. L. ; Langan, P. ; Kovalevsky, A. ; Dealwis, C. G. (Corresponding author)

2021
ACS Washington, DC

Please use a persistent id in citations: doi:10.1021/acscatal.1c00417

Abstract: Acid−base catalysis, which involves one or more proton transfer reactions, is a chemicalmechanism commonly employed by many enzymes. The molecular basis for catalysis is often derived fromstructures determined at the optimal pH for enzyme activity. However, direct observation of protons fromexperimental structures is quite difficult; thus, a complete mechanistic description for most enzymesremains lacking. Dihydrofolate reductase (DHFR) exemplifies general acid−base catalysis, requiringhydride transfer and protonation of its substrate, DHF, to form the product, tetrahydrofolate (THF).Previous X-ray and neutron crystal structures coupled with theoretical calculations have proposed thatsolvent mediates the protonation step. However, visualization of a proton transfer has been elusive. Basedon a 2.1 Å resolution neutron structure of a pseudo-Michaelis complex of E. coli DHFR determined atacidic pH, we report the direct observation of the catalytic proton and its parent solvent molecule.Comparison of X-ray and neutron structures elucidated at acidic and neutral pH reveals dampeneddynamics at acidic pH, even for the regulatory Met20 loop. Guided by the structures and calculations, wepropose a mechanism where dynamics are crucial for solvent entry and protonation of substrate. Thismechanism invokes the release of a sole proton from a hydronium (H3O+) ion, its pathway through a narrow channel that sterically hinders the passage of water, and the ultimate protonation of DHF at the N5 atom.

Keyword(s): Health and Life (1st) ; Biology (2nd)

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Contributing Institute(s):

1. BIODIFF (BIODIFF)

Experiment(s):

1. BIODIFF: Diffractometer for large unit cells (NL1)

Appears in the scientific report 2021

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Database coverage:
; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Essential Science Indicators ; IF >= 10 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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