Journal Article

FZJ-2019-00783

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Understanding the pH-Dependent Reaction Mechanism of a Glycoside Hydrolase Using High-Resolution X-ray and Neutron Crystallographyülcih

Li, Z. ; Zhang, X. ; Wang, Q. ; Li, C. ; Zhang, N. ; Zhang, X. ; Xu, B. ; Ma, B. ; Schrader, T. E.FZJ* ; Coates, L. ; Kovalevsky, A. ; Huang, Y. ; Wan, Q. (Corresponding author)

2018
ACS Washington, DC

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Please use a persistent id in citations: doi:10.1021/acscatal.8b01472

Abstract: Glycoside hydrolases (GHs) commonly use the retaining or inverting mechanisms to hydrolyze carbohydrates, and the rates of catalysis are usually pH dependent. Deeper understanding of these pH-dependent reaction mechanisms is of great importance for protein engineering and drug design. We used high-resolution X-ray crystallography to analyze the sugar ring configurations of an oligosaccharide ligand during hydrolysis for the family 11 GH, and the results support the 1S3 → 4H3 → 4C1 conformational itinerary. These results indicate that sugar ring flexibility may help to distort and break the glycosidic bond. Constant pH molecular dynamics simulations and neutron crystallography demonstrate that the catalytic glutamate residue (E177) has alternate conformational changes to transfer a proton to cleave the glycosidic bond. Furthermore, a neutron crystallography analysis shows that the H-bond length between E177 and its nearby tyrosine residue (Y88) is shortened when the pH increases, preventing E177 from rotating downward and obtaining a proton from the solvent for catalysis. This result indicates that the H-bond length variation may play a key role in the pH-dependent reaction mechanism. In summary, our results demonstrate that both sugar ring flexibility and protein dynamics are important in the pH-dependent reaction mechanism and may help to engineer GHs with different pH optima.

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

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Contributing Institute(s):

1. JCNS-FRM-II (JCNS-FRM-II)
2. Neutronenstreuung (JCNS-1)

Research Program(s):

1. 6G15 - FRM II / MLZ (POF3-6G15) (POF3-6G15)
2. 6G4 - Jülich Centre for Neutron Research (JCNS) (POF3-623) (POF3-623)
3. 6215 - Soft Matter, Health and Life Sciences (POF3-621) (POF3-621)

Experiment(s):

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

Appears in the scientific report 2018

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

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