8K2F

Crystal structure of Group 1 oligosaccharide-releasing beta-N-acetylgalactosaminidase NgaCa from Cohnella abietis, apo 1 form

Summary for 8K2F

• Entry DOI: 10.2210/pdb8k2f/pdb
• Descriptor: Oligosaccharide-releasing beta-N-acetylgalactosaminidase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: glycoside hydrolase, hydrolase
• Biological source: Cohnella abietis
• Total number of polymer chains: 1
• Total formula weight: 58162.02

Authors

Sumida, T.,Fushinobu, S. (deposition date: 2023-07-12, release date: 2024-04-24, Last modification date: 2024-05-22)

Primary citation

Sumida, T.,Hiraoka, S.,Usui, K.,Ishiwata, A.,Sengoku, T.,Stubbs, K.A.,Tanaka, K.,Deguchi, S.,Fushinobu, S.,Nunoura, T.
Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Nat Commun, 15:3543-3543, 2024

PubMed Abstract: β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.

PubMed: 38730244
DOI: 10.1038/s41467-024-47653-2

Experimental method

X-RAY DIFFRACTION (1.75 Å)