6FAR | pdb_00006far

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-mannoimidazole

• PDB DOI: https://doi.org/10.2210/pdb6FAR/pdb

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


• Deposited: 2017-12-16 Released: 2018-03-21 
• Deposition Author(s): Fernandes, P.Z., Petricevic, M., Sobala, L.F., Davies, G.J., Williams, S.J.
• Funding Organization(s): European Research Council, Australian Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.162 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-alpha-1,2-Mannanases.

Fernandes, P.Z., Petricevic, M., Sobala, L., Davies, G.J., Williams, S.J.

(2018) Chemistry 24: 7464-7473

• PubMed: 29508463 
• DOI: https://doi.org/10.1002/chem.201800435
• Primary Citation Related Structures: 
  6FAM, 6FAR


• PubMed Abstract: 
  

  endo-α-1,2-Mannosidases and -mannanases, members of glycoside hydrolase family 99 (GH99), cleave α-Glc/Man-1,3-α-Man-OR structures within mammalian N-linked glycans and fungal α-mannan, respectively. They are proposed to act through a two-step mechanism involving a 1,2-anhydrosugar "epoxide" intermediate incorporating two conserved catalytic carboxylates. In the first step, one carboxylate acts as a general base to deprotonate the 2-hydroxy group adjacent to the fissile glycosidic bond, and the other provides general acid assistance to the departure of the aglycon. We report herein the synthesis of two inhibitors designed to interact with either the general base (α-mannosyl-1,3-(2-aminodeoxymannojirimycin), Man2NH ₂ DMJ) or the general acid (α-mannosyl-1,3-mannoimidazole, ManManIm). Modest affinities were observed for an endo-α-1,2-mannanase from Bacteroides thetaiotaomicron. Structural studies revealed that Man2NH ₂ DMJ binds like other iminosugar inhibitors, which suggests that the poor inhibition shown by this compound is not a result of a failure to achieve the expected interaction with the general base, but rather the reduction in basicity of the endocyclic nitrogen caused by introduction of a vicinal, protonated amine at C2. ManManIm binds with the imidazole headgroup distorted downwards, a result of an unfavourable interaction with a conserved active site tyrosine. This study has identified important limitations associated with mechanism-inspired inhibitor design for GH99 enzymes.

---

Organizational Affiliation: 
• School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic, 3010, Australia.
York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.

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: 44.31 kDa 
• Atom Count: 3,598 
• Modeled Residue Count: 346 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MVL (Subject of Investigation/LOI)	C [auth A]	(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL C8 H12 N2 O4 RZRDQZQPTISYKY-JWXFUTCRSA-N
MAN	B [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.162 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.4446244

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.619	α = 90
b = 108.619	β = 90
c = 67.766	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Fernandes, P.Z., Petricevic, M., Sobala, L.F., Davies, G.J., Williams, S.J.

---

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Australian Research Council	Australia	FT130100103
Australian Research Council	Australia	DP120101396

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-02-03
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description