Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism

Abstract

Background:The endo-␣-D-N-acetylgalactosaminidase SpGH101 from Streptococcus pneumoniae hydrolyzes the O-linked T-antigen from proteins. Results: SpGH101 displays an unusual conformational change on substrate binding and a distinctive arrangement of its catalytic machinery. Conclusion: Substrate hydrolysis proceeds through a retaining mechanism with a proton shuttle. Significance: This is the first evidence of proton shuttle in a retaining glycoside hydrolase.

Glycan‐metabolizing enzymes in microbe–host interactions: the Streptococcus pneumoniae paradigm

“…The multimodular structure of Eng consists of seven distinct domains, including the catalytic GH101 domain and a family 32 CBM [124,125]. Biochemical and structural investigation of Eng in complex with unhydrolyzed substrate identified the catalytic residues and revealed that the protein bound only to its known disaccharide substrate [125,126]. Biochemical and structural investigation of Eng in complex with unhydrolyzed substrate identified the catalytic residues and revealed that the protein bound only to its known disaccharide substrate [125,126].…”

“…Its crystal structure revealed that the protein contains a further three putative CBMs in addition to the CBM32 [124]. Biochemical and structural investigation of Eng in complex with unhydrolyzed substrate identified the catalytic residues and revealed that the protein bound only to its known disaccharide substrate [125,126]. Ultimately, the fate of the disaccharide released by Eng is not knownno transporter has been identified and none of the GHs produced by S. pneumoniae are known to cleave Gal-b-(1?3)-GalNAc.…”

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum

“…The distance between Asp411 and the O1 of GlcNAc (3.0 Å ) does not exclude a direct proton transfer mechanism, but the presence of the bridging water molecule suggests a mechanism involving water-mediated proton transfer ( Figure S5). Of note is that the Grotthuss proton shuttle mechanism has been suggested for GH families 6, 101, and 124 (Bras et al, 2011;Gregg et al, 2015;Koivula et al, 2002).…”

Catalytic and structural properties of pheophytinase, the phytol esterase involved in chlorophyll breakdown

“…If this is true, we must assume that presence of Mg in chlorophyll a abolished the catalytic cycle. A reason for this could lie in the inability of the enzyme to properly close the lid domain, when chlorophyll a is bound, to fully engage the substrate in the active site as a prerequisite for catalytic activity ( Gregg et al , 2015 ). Such steric hindrance could result from possible coordination of the Mg present in chlorophyll with certain amino acid residues within PPH.…”