6JQF

Crystallization analysis of a beta-N-acetylhexosaminidase (Am2136) from Akkermansia muciniphila

Summary for 6JQF

• Entry DOI: 10.2210/pdb6jqf/pdb
• Descriptor: Glycoside hydrolase, family 20, catalytic core, MAGNESIUM ION, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: keywords:beta-n-acetylhexosaminidas;crystallographic evidence; catalytic mechanism; akkermansia muciniphila;, hydrolase
• Biological source: Akkermansia muciniphila (strain ATCC BAA-835 / Muc)
• Total number of polymer chains: 1
• Total formula weight: 82827.73

Authors

Zhang, M.,Chen, X. (deposition date: 2019-03-31, release date: 2019-12-11, Last modification date: 2024-10-09)

Primary citation

Chen, X.,Li, M.,Wang, Y.,Tang, R.,Zhang, M.
Biochemical characteristics and crystallographic evidence for substrate-assisted catalysis of a beta-N-acetylhexosaminidase in Akkermansia muciniphila.
Biochem.Biophys.Res.Commun., 517:29-35, 2019

PubMed Abstract: In this paper, we characterized Am2136 as a β-N-acetylhexosaminidase from Akkermansia muciniphila to perform the biochemical characteristics and the crystal structure of selenomethionine-labeled Am2136 with GlcNAc complex. Crystallographic evidence suggests that an oxazolinium ion was formed intermediately by the 2-acetamido group during the substrate-assisted catalytic procedure. Structural and kinetic analysis of native Am2136 and D412A, E413A mutants were investigated and the results revealed substantial difference. The K/K value of D412A was decreased 4297-fold compared to native Am2136 revealed that mutation of Asp-412 results in preventing the 2-acetamido substituent from providing anchimeric assistance and thus reducing the catalytic efficiency. Moreover, Am2136 has a wide dependence on pH and temperature, while sensitive to divalent metal ions such as Ca and Mn. These biochemical and crystallographic results provide evidences that Asp-412 residue assists to orient the 2-acetamido group for catalysis. Based on crystallographic evidence and sequence alignment with other GH family 20 enzymes, Asp-412 residue is possibly fundamental for Am2136 during substrate-assisted catalysis.

PubMed: 31345574
DOI: 10.1016/j.bbrc.2019.06.150

Experimental method

X-RAY DIFFRACTION (1.9 Å)