9FYM
Lacto-N-biosidase from Treponema denticola ATCC 35405
Summary for 9FYM
| Entry DOI | 10.2210/pdb9fym/pdb |
| Descriptor | Glycoside hydrolase family 20 catalytic domain-containing protein, IMIDAZOLE, SODIUM ION, ... (5 entities in total) |
| Functional Keywords | lacto-n-biosidase, gh20, hydrolase |
| Biological source | Treponema denticola ATCC 35405 |
| Total number of polymer chains | 1 |
| Total formula weight | 38062.09 |
| Authors | Vuillemin, M.,Siebenhaar, S.,Zeuner, B.,Morth, J.P. (deposition date: 2024-07-03, release date: 2024-10-09) |
| Primary citation | Vuillemin, M.,Muschiol, J.,Zhang, Y.,Holck, J.,Barrett, K.,Morth, J.P.,Meyer, A.S.,Zeuner, B. Discovery of Lacto-N-biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights. Chembiochem, :e202400710-e202400710, 2024 Cited by PubMed Abstract: The glycoside hydrolase family 20 (GH20) predominantly features N-acetylhexosaminidases (EC 3.2.1.52), with only few known lacto-N-biosidases (EC 3.2.1.140; LNBases). LNBases catalyze the degradation of lacto-N-tetraose (LNT), a prominent component of human milk oligosaccharides, thereby supporting a healthy infant gut microbiome development. We investigated GH20 diversity to discover novel enzymes that release disaccharides such as lacto-N-biose (LNB). Our approach combined peptide clustering, sequence analysis, and 3D structure model evaluation to assess active site topologies, focusing on the presence of a subsite -2. Five LNBases were active on pNP-LNB and four showed activity on LNT. One enzyme displayed activity on both pNP-LacNAc and pNP-LNB, establishing the first report of N-acetyllactosaminidase (LacNAcase) activity. Exploration of this enzyme cluster led to the identification of four additional enzymes sharing this dual substrate specificity. Comparing the determined crystal structure of a specific LNBase (TrpyGH20) and the first crystal structure of an enzyme with dual LacNAcase/LNBase activity (TrdeGH20) revealed a highly conserved subsite -1, common to GH20 enzymes, while the -2 subsites varied significantly. TrdeGH20 had a wider subsite -2, accommodating Gal with both β1,4- and β1,3-linkages to the GlcNAc in subsite -1. Biotechnological applications of these enzymes may include structural elucidation of complex carbohydrates and glycoengineering. PubMed: 39239753DOI: 10.1002/cbic.202400710 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.34 Å) |
Structure validation
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