7Q20

Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) in complex with blood group A trisaccharide

This is a non-PDB format compatible entry.

Summary for 7Q20

• Entry DOI: 10.2210/pdb7q20/pdb
• Descriptor: Ruminococcus gnavus endogalactosidase GH98, alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: endogalactosidase, glycoside hydrolase, hydrolase
• Biological source: Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)
• Total number of polymer chains: 2
• Total formula weight: 191052.72

Authors

Owen, C.D.,Wu, H.,Crost, E.H.,van Bakel, W.,Gascuena, A.M.,Latousakis, D.,Hicks, T.,Walpole, S.,Urbanowicz, P.A.,Ndeh, D.,Monaco, S.,Salom, L.S.,Griffiths, R.,Colvile, A.,Spencer, D.I.R.,Walsh, M.A.,Angulo, J.,Juge, N. (deposition date: 2021-10-22, release date: 2022-02-02, Last modification date: 2024-01-31)

Primary citation

Wu, H.,Crost, E.H.,Owen, C.D.,van Bakel, W.,Martinez Gascuena, A.,Latousakis, D.,Hicks, T.,Walpole, S.,Urbanowicz, P.A.,Ndeh, D.,Monaco, S.,Sanchez Salom, L.,Griffiths, R.,Reynolds, R.S.,Colvile, A.,Spencer, D.I.R.,Walsh, M.,Angulo, J.,Juge, N.
The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract.
Plos Biol., 19:e3001498-e3001498, 2021

PubMed Abstract: The human gut symbiont Ruminococcus gnavus displays strain-specific repertoires of glycoside hydrolases (GHs) contributing to its spatial location in the gut. Sequence similarity network analysis identified strain-specific differences in blood-group endo-β-1,4-galactosidase belonging to the GH98 family. We determined the substrate and linkage specificities of GH98 from R. gnavus ATCC 29149, RgGH98, against a range of defined oligosaccharides and glycoconjugates including mucin. We showed by HPAEC-PAD and LC-FD-MS/MS that RgGH98 is specific for blood group A tetrasaccharide type II (BgA II). Isothermal titration calorimetry (ITC) and saturation transfer difference (STD) NMR confirmed RgGH98 affinity for blood group A over blood group B and H antigens. The molecular basis of RgGH98 strict specificity was further investigated using a combination of glycan microarrays, site-directed mutagenesis, and X-ray crystallography. The crystal structures of RgGH98 in complex with BgA trisaccharide (BgAtri) and of RgGH98 E411A with BgA II revealed a dedicated hydrogen network of residues, which were shown by site-directed mutagenesis to be critical to the recognition of the BgA epitope. We demonstrated experimentally that RgGH98 is part of an operon of 10 genes that is overexpresssed in vitro when R. gnavus ATCC 29149 is grown on mucin as sole carbon source as shown by RNAseq analysis and RT-qPCR confirmed RgGH98 expression on BgA II growth. Using MALDI-ToF MS, we showed that RgGH98 releases BgAtri from mucin and that pretreatment of mucin with RgGH98 confered R. gnavus E1 the ability to grow, by enabling the E1 strain to metabolise BgAtri and access the underlying mucin glycan chain. These data further support that the GH repertoire of R. gnavus strains enable them to colonise different nutritional niches in the human gut and has potential applications in diagnostic and therapeutics against infection.

PubMed: 34936658
DOI: 10.1371/journal.pbio.3001498

Experimental method

X-RAY DIFFRACTION (1.95 Å)