9EP5

GH191 family Alpha-Galactosaminidase from Environmental sample (99.2% identity to Myxococcus fulvus enzyme)

Summary for 9EP5

• Entry DOI: 10.2210/pdb9ep5/pdb
• Descriptor: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein, SULFATE ION (3 entities in total)
• Functional Keywords: gh114 family, crystal pathology, environmental sample, hydrolase
• Biological source: environmental samples
• Total number of polymer chains: 2
• Total formula weight: 65774.84

Authors

Roth, C.,Moroz, O.V.,Miranda, S.A.D.,Jahn, L.,Blagova, E.,Lebedev, A.A.,Segura, D.R.,Stringer, M.A.,Friis, E.P.,Davies, G.J.,Wilson, K.S. (deposition date: 2024-03-17, release date: 2025-04-23, Last modification date: 2025-05-14)

Primary citation

Roth, C.,Moroz, O.V.,Miranda, S.A.D.,Jahn, L.,Blagova, E.V.,Lebedev, A.A.,Segura, D.R.,Stringer, M.A.,Friis, E.P.,Franco Cairo, J.P.L.,Davies, G.J.,Wilson, K.S.
Structures of alpha-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases.
Acta Crystallogr D Struct Biol, 81:234-251, 2025

PubMed Abstract: Endo-galactosaminidases are an underexplored family of enzymes involved in the degradation of galactosaminogalactan (GAG) and other galactosamine-containing cationic exopolysaccharides produced by fungi and bacteria. These exopolysaccharides are part of the cell wall and extracellular matrix of microbial communities. Currently, these galactosaminidases are found in three distinct CAZy families: GH114, GH135 and GH166. Despite the widespread occurrence of these enzymes in nearly all bacterial and fungal clades, only limited biochemical and structural data are available for these three groups. To expand our knowledge of endo-galactosaminidases, we selected several sequences predicted to encode endo-galactosaminidases and produced them recombinantly for structural and functional studies. Only very few predicted proteins could be produced in soluble form, and activity against bacterial Pel (pellicle) polysaccharide could only be confirmed for one enzyme. Here, we report the structures of two bacterial and one fungal enzyme. Whereas the fungal enzyme belongs to family GH114, the two bacterial enzymes do not lie in the current GH families but instead define a new family, GH191. During structure solution we realized that crystals of all three enzymes had various defects including twinning and partial disorder, which in the case of a more severe pathology in one of the structures required the design of a specialized refinement/model-building protocol. Comparison of the structures revealed several features that might be responsible for the described activity pattern and substrate specificity compared with other GAG-degrading enzymes.

PubMed: 40232846
DOI: 10.1107/S2059798325002864

Experimental method

X-RAY DIFFRACTION (1.64 Å)