Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 191.09 kDa 
• Atom Count: 14629 
• Modelled Residue Count: 1695 
• Deposited Residue Count: 1698 
• Unique protein chains: 1

7PMO

Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)

• PDB DOI: 10.2210/pdb7PMO/pdb

• Classification: HYDROLASE
• Organism(s): [Ruminococcus] gnavus ATCC 29149
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-02 Released: 2022-02-02 
• Deposition Author(s): 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.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

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.

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.

(2021) PLoS Biol 19: e3001498-e3001498

• PubMed: 34936658 
• DOI: 10.1371/journal.pbio.3001498
• Primary Citation of Related Structures:  
  7PMO, 7Q1W, 7Q20


• 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.

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Organizational Affiliation: 

Quadram Institute Bioscience, Norwich, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ruminococcus gnavus endogalactosidase GH98	A [auth D], B [auth G]	849	[Ruminococcus] gnavus ATCC 29149	Mutation(s): 0  Gene Names: RUMGNA_03119
UniProt
Find proteins for A7B6A6 (Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9)) Explore A7B6A6  Go to UniProtKB:  A7B6A6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth D], E [auth D], F [auth D], G [auth D], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	K [auth D], R [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth D], I [auth D], J [auth D], Q [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.313	α = 90
b = 85.566	β = 98.94
c = 112.628	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-09-02 
• Released Date: 2022-02-02 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release