6WB7

Acarbose Kinase AcbK as a Complex with Acarbose and AMP-PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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Literature

The human microbiome encodes resistance to the antidiabetic drug acarbose.

Balaich, J.Estrella, M.Wu, G.Jeffrey, P.D.Biswas, A.Zhao, L.Korennykh, A.Donia, M.S.

(2021) Nature 600: 110-115

  • DOI: https://doi.org/10.1038/s41586-021-04091-0
  • Primary Citation of Related Structures:  
    6WB4, 6WB5, 6WB7

  • PubMed Abstract: 

    The human microbiome encodes a large repertoire of biochemical enzymes and pathways, most of which remain uncharacterized. Here, using a metagenomics-based search strategy, we discovered that bacterial members of the human gut and oral microbiome encode enzymes that selectively phosphorylate a clinically used antidiabetic drug, acarbose 1,2 , resulting in its inactivation. Acarbose is an inhibitor of both human and bacterial α-glucosidases 3 , limiting the ability of the target organism to metabolize complex carbohydrates. Using biochemical assays, X-ray crystallography and metagenomic analyses, we show that microbiome-derived acarbose kinases are specific for acarbose, provide their harbouring organism with a protective advantage against the activity of acarbose, and are widespread in the microbiomes of western and non-western human populations. These results provide an example of widespread microbiome resistance to a non-antibiotic drug, and suggest that acarbose resistance has disseminated in the human microbiome as a defensive strategy against a potential endogenous producer of a closely related molecule.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acarbose 7(IV)-phosphotransferase
A, B, C, D
319Actinoplanes sp. SE50/110Mutation(s): 0 
Gene Names: acbKACPL_3675
EC: 2.7.1.187
UniProt
Find proteins for Q8RMD4 (Actinoplanes sp. (strain ATCC 31044 / CBS 674.73 / SE50/110))
Explore Q8RMD4 
Go to UniProtKB:  Q8RMD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RMD4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, F, G, H
3N/AN/A
Glycosylation Resources
GlyTouCan:  G66431MI
GlyCosmos:  G66431MI
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
S [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B],
P [auth C],
R [auth C],
T [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B],
Q [auth C],
U [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.545α = 89.06
b = 50.268β = 80.18
c = 127.794γ = 71.81
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2021-12-15
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description