5M03

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.

Petricevic, M.Sobala, L.F.Fernandes, P.Z.Raich, L.Thompson, A.J.Bernardo-Seisdedos, G.Millet, O.Zhu, S.Sollogoub, M.Jimenez-Barbero, J.Rovira, C.Davies, G.J.Williams, S.J.

(2017) J Am Chem Soc 139: 1089-1097

  • DOI: 10.1021/jacs.6b10075
  • Primary Citation of Related Structures:  
    5LYR, 5M03, 5M17, 5M3W, 5M5D, 5MC8, 5MEL

  • PubMed Abstract: 
  • Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics ...

    Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively. These enzymes are proposed to act via a 1,2-anhydrosugar "epoxide" mechanism that proceeds through an unusual conformational itinerary. Here, we explore how shape and charge contribute to binding of diverse inhibitors of these enzymes. We report the synthesis of neutral dideoxy, glucal and cyclohexenyl disaccharide inhibitors, their binding to GH99 endo-α-1,2-mannanases, and their structural analysis by X-ray crystallography. Quantum mechanical calculations of the free energy landscapes reveal how the neutral inhibitors provide shape but not charge mimicry of the proposed intermediate and transition state structures. Building upon the knowledge of shape and charge contributions to inhibition of family GH99 enzymes, we design and synthesize α-Man-1,3-noeuromycin, which is revealed to be the most potent inhibitor (K D 13 nM for Bacteroides xylanisolvens GH99 enzyme) of these enzymes yet reported. This work reveals how shape and charge mimicry of transition state features can enable the rational design of potent inhibitors.


    Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranoseB 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

Download Ideal Coordinates CCD File 
E [auth A](2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
C6 H13 N O4
BHOYFRIRWXBNHP-ZXXMMSQZSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900111
Query on PRD_900111
B2alpha-alpha-mannobioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.033α = 90
b = 108.033β = 90
c = 67.45γ = 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
Spanish Ministry of Economy and CompetitivenessSpainCTQ2014-55174
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-64597-C2-1P
Spanish Ministry of Economy and CompetitivenessSpainCTQ2015-68756-R
Generalitat de CatalunyaSpain2014SGR-987

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary