7WDT | pdb_00007wdt

6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S

• PDB DOI: https://doi.org/10.2210/pdb7WDT/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum JCM 1254
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-12-22 Released: 2022-12-28 
• Deposition Author(s): Yamada, C., Kashima, T., Fushinobu, S., Katoh, T., Katayama, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.200 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.

Katoh, T., Yamada, C., Wallace, M.D., Yoshida, A., Gotoh, A., Arai, M., Maeshibu, T., Kashima, T., Hagenbeek, A., Ojima, M.N., Takada, H., Sakanaka, M., Shimizu, H., Nishiyama, K., Ashida, H., Hirose, J., Suarez-Diez, M., Nishiyama, M., Kimura, I., Stubbs, K.A., Fushinobu, S., Katayama, T.

(2023) Nat Chem Biol 19: 778-789

• PubMed: 36864192 
• DOI: https://doi.org/10.1038/s41589-023-01272-y
• Primary Citation Related Structures: 
  7WDT, 7WDU


• PubMed Abstract: 
  

  Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.

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Organizational Affiliation: 
• Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.
Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
Department of Microbiology, School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan.
Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan.
School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga, Japan.
Department of Food and Nutrition, Kyoto Women's University, Kyoto, Japan.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. [e-mail].
Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 90.42 kDa 
• Atom Count: 6,897 
• Modeled Residue Count: 819 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A	830	Bifidobacterium bifidum JCM 1254	Mutation(s): 0  Gene Names: bbhII EC: 3.2.1.52
UniProt
Find proteins for D4QAP5 (Bifidobacterium bifidum) Explore D4QAP5  Go to UniProtKB:  D4QAP5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGS (Subject of Investigation/LOI)	B [auth A]	2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose C8 H15 N O9 S WJFVEEAIYIOATH-FMDGEEDCSA-N
NGY (Subject of Investigation/LOI)	C [auth A]	2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose C8 H15 N O9 S WJFVEEAIYIOATH-PVFLNQBWSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.200 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.131	α = 90
b = 57.879	β = 98.59
c = 98.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Yamada, C., Kashima, T., Fushinobu, S., Katoh, T., Katayama, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19K05789
Japan Society for the Promotion of Science (JSPS)	Japan	21H02116

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2023-03-15
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Data collection, Structure summary