5U08

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acsinfecdis.7b00068
  • Primary Citation of Related Structures:  

  • 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 enz ...

    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 Molecular Microbiology, Washington University School of Medicine , 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , Health Research Innovation Center, 3280 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.,Department of Biomedical Engineering, Washington University in St. Louis , 1 Brookings Drive, St. Louis, Missouri 63130-6100, United States.,Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Room 333, Toronto, Ontario M5S 3E5, Canada.,Department of Medical Biophysics, University of Toronto , 101 College Street, Room 4-601, Toronto, Ontario M5G 1L7, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary , 2C66 Health Research Innovation Center, 3280 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.,Department of Pathology and Immunology, Washington University School of Medicine , 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States.,Center for Genome Sciences & Systems Biology, Washington University School of Medicine , 4515 McKinley Avenue, Room 5314, St. Louis, Missouri 63110, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
aminoglycoside acetyltransferase meta-AAC0020
A, B, C, D
157uncultured bacteriumMutation(s): 1 
Find proteins for A0A059WZ16 (uncultured bacterium)
Go to UniProtKB:  A0A059WZ16
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SIS
Query on SIS

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Download CCD File 
A, C, D
(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
Sisomicin
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 46.295α = 71.76
b = 53.035β = 75.61
c = 78.676γ = 88.69
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesHHSN272201200026C

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2019-04-03
    Type: Data collection, Database references, Structure summary