6FAM

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-2-aminodeoxymannojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1002/chem.201800435
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 71A385Bacteroides xylanisolvens XB1AMutation(s): 0 
Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Explore D6D1V7 
Go to UniProtKB:  D6D1V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6D1V7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
G63
Query on G63

Download Ideal Coordinates CCD File 
D [auth A] mannose-alpha-1,3-2-aminodeoxymannojirimycin
C6 H14 N2 O3
GFTGLZPGRKFGDU-KVTDHHQDSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.101α = 90
b = 108.101β = 90
c = 67.507γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom322942
Australian Research CouncilAustraliaFT130100103
Australian Research CouncilAustraliaDP120101396

Revision History  (Full details and data files)

  • 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