8TCD

Structure of Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An alternative broad-specificity pathway for glycan breakdown in bacteria.

Nasseri, S.A.Lazarski, A.C.Lemmer, I.L.Zhang, C.Y.Brencher, E.Chen, H.M.Sim, L.Panwar, D.Betschart, L.Worrall, L.J.Brumer, H.Strynadka, N.C.J.Withers, S.G.

(2024) Nature 631: 199-206

  • DOI: https://doi.org/10.1038/s41586-024-07574-y
  • Primary Citation of Related Structures:  
    8TCD, 8TCR, 8TCS, 8TCT, 8TDA, 8TDE, 8TDF, 8TDH, 8TDI

  • PubMed Abstract: 

    The vast majority of glycosidases characterized to date follow one of the variations of the 'Koshland' mechanisms 1 to hydrolyse glycosidic bonds through substitution reactions. Here we describe a large-scale screen of a human gut microbiome metagenomic library using an assay that selectively identifies non-Koshland glycosidase activities 2 . Using this, we identify a cluster of enzymes with extremely broad substrate specificities and thoroughly characterize these, mechanistically and structurally. These enzymes not only break glycosidic linkages of both α and β stereochemistry and multiple connectivities, but also cleave substrates that are not hydrolysed by standard glycosidases. These include thioglycosides, such as the glucosinolates from plants, and pseudoglycosidic bonds of pharmaceuticals such as acarbose. This is achieved through a distinct mechanism of hydrolysis that involves oxidation/reduction and elimination/hydration steps, each catalysed by enzyme modules that are in many cases interchangeable between organisms and substrate classes. Homologues of these enzymes occur in both Gram-positive and Gram-negative bacteria associated with the gut microbiome and other body parts, as well as other environments, such as soil and sea. Such alternative step-wise mechanisms appear to constitute largely unrecognized but abundant pathways for glycan degradation as part of the metabolism of carbohydrates in bacteria.


  • Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sugar phosphate isomeraseA [auth B],
B [auth C],
C [auth D],
D [auth A]
286AlistipesMutation(s): 0 
Gene Names: A5CPYCFAH4_05830
UniProt
Find proteins for A0A9P3ZKE6 (Alistipes onderdonkii)
Explore A0A9P3ZKE6 
Go to UniProtKB:  A0A9P3ZKE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9P3ZKE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B],
I [auth C],
K [auth D],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth B],
N [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO
Query on CO

Download Ideal Coordinates CCD File 
E [auth B],
H [auth C],
J [auth D],
L [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.574α = 90
b = 112.608β = 90
c = 209.335γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Database references