6HMG

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine)

• PDB DOI: https://doi.org/10.2210/pdb6HMG/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-12 Released: 2018-09-26 
• Deposition Author(s): Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.
• Funding Organization(s): European Research Council, Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-alpha-mannosidase.

Lu, D., Zhu, S., Sobala, L.F., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Jimenez-Barbero, J., Davies, G.J., Sollogoub, M.

(2018) Org Lett 20: 7488-7492

• PubMed: 30427198 
• DOI: https://doi.org/10.1021/acs.orglett.8b03260
• Primary Citation of Related Structures:  
  6HMG, 6HMH


• PubMed Abstract: 
  

  Understanding the enzyme reaction mechanism can lead to the design of enzyme inhibitors. A Claisen rearrangement was used to allow conversion of an α-1,4-disaccharide into an α-1,3-linked glycosyl carbasugar to target the endo-α-mannosidase from the GH99 glycosidase family, which, unusually, is believed to act through a 1,2-anhydrosugar "epoxide" intermediate. Using NMR and X-ray crystallography, it is shown that glucosyl carbasugar α-aziridines can act as reasonably potent endo-α-mannosidase inhibitors, likely by virtue of their shape mimicry and the interactions of the aziridine nitrogen with the conserved catalytic acid/base of the enzyme active site.

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Organizational Affiliation: 

Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France.

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: 44.33 kDa 
• Atom Count: 3,491 
• Modelled Residue Count: 349 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A	385	Bacteroides xylanisolvens XB1A	Mutation(s): 0  Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	D [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
GDQ (Subject of Investigation/LOI)	C [auth A]	(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol C7 H13 N O3 JACJTGDBUDQHPY-VOQCIKJUSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.4431701

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.772	α = 90
b = 108.772	β = 90
c = 67.703	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2017-85496-P
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-64597-C2-1P

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 2.0: 2018-12-19
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-04-24
  Changes: Data collection, Database references
• Version 2.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 2.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description