9FYN

Lacto-N-biosidase from Trueperella pyogenes

Summary for 9FYN

• Entry DOI: 10.2210/pdb9fyn/pdb
• Descriptor: lacto-n-biosidase GH20, NICKEL (II) ION (3 entities in total)
• Functional Keywords: lacto-n-biosidase, gh20, hydrolase
• Biological source: Trueperella pyogenes
• Total number of polymer chains: 1
• Total formula weight: 84962.51

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

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: 39239753
DOI: 10.1002/cbic.202400710

Experimental method

X-RAY DIFFRACTION (1.79 Å)