Crystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with trehalose

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report

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Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes.

Xu, Z.Stogios, P.J.Quaile, A.T.Forsberg, K.J.Patel, S.Skarina, T.Houliston, S.Arrowsmith, C.Dantas, G.Savchenko, A.

(2017) ACS Infect Dis 3: 653-665

  • DOI: https://doi.org/10.1021/acsinfecdis.7b00068
  • Primary Citation of Related Structures:  
    5F46, 5F47, 5F48, 5F49, 5U08

  • PubMed Abstract: 

    Aminoglycoside N-acetyltransferases (AACs) confer resistance against the clinical use of aminoglycoside antibiotics. The origin of AACs can be traced to environmental microbial species representing a vast reservoir for new and emerging resistance enzymes, which are currently undercharacterized. Here, we performed detailed structural characterization and functional analyses of four metagenomic AAC (meta-AACs) enzymes recently identified in a survey of agricultural and grassland soil microbiomes ( Forsberg et al. Nature 2014 , 509 , 612 ). These enzymes are new members of the Gcn5-Related-N-Acetyltransferase superfamily and confer resistance to the aminoglycosides gentamicin C, sisomicin, and tobramycin. Moreover, the meta-AAC0020 enzyme demonstrated activity comparable with an AAC(3)-I enzyme that serves as a model AAC enzyme identified in a clinical bacterial isolate. The crystal structure of meta-AAC0020 in complex with sisomicin confirmed an unexpected AAC(6') regiospecificity of this enzyme and revealed a drug binding mechanism distinct from previously characterized AAC(6') enzymes. Together, our data highlights the presence of highly active antibiotic-modifying enzymes in the environmental microbiome and reveals unexpected diversity in substrate specificity. These observations of additional AAC enzymes must be considered in the search for novel aminoglycosides less prone to resistance.

  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Room 333, Toronto, Ontario M5S 3E5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
aminoglycoside acetyltransferase meta-AAC0020
A, B
157uncultured bacteriumMutation(s): 0 
Find proteins for A0A059WZ16 (uncultured bacterium)
Explore A0A059WZ16 
Go to UniProtKB:  A0A059WZ16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059WZ16
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.001α = 90
b = 53.954β = 105.19
c = 46.023γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXmodel building
Cootmodel building

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Structure summary
  • Version 1.2: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 1.3: 2019-04-03
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-03-06
    Changes: Data collection, Database references, Structure summary