Crystal structure of aminoglycoside acetyltransferase AAC(2')-Ia in complex with N2'-acetylgentamicin C1A and coenzyme A

Experimental Data Snapshot

  • Resolution: 2.48 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes.

Cox, G.Ejim, L.Stogios, P.J.Koteva, K.Bordeleau, E.Evdokimova, E.Sieron, A.O.Savchenko, A.Serio, A.W.Krause, K.M.Wright, G.D.

(2018) ACS Infect Dis 4: 980-987

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00001
  • Primary Citation of Related Structures:  
    5US1, 6CD7

  • PubMed Abstract: 

    Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.

  • Organizational Affiliation

    M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine , McMaster University , 1280 Main Street West , Hamilton , Ontario L8N 4K1 , Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside 2'-N-acetyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
189Providencia stuartiiMutation(s): 0 
Gene Names: aac
Find proteins for Q52424 (Providencia stuartii)
Explore Q52424 
Go to UniProtKB:  Q52424
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52424
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ACO

Download Ideal Coordinates CCD File 
C23 H38 N7 O17 P3 S
Query on COA

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BA [auth I],
HA [auth L],
U [auth E]
C21 H36 N7 O16 P3 S
Query on 8MM

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AA [auth I]
EA [auth K]
GA [auth L]
M [auth A]
O [auth B]
AA [auth I],
EA [auth K],
GA [auth L],
M [auth A],
O [auth B],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Y [auth H]
(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-(acetylamino)-6-amino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
C21 H41 N5 O8
Query on TAR

Download Ideal Coordinates CCD File 
DA [auth J],
N [auth A],
S [auth D],
W [auth F],
Z [auth H]
C4 H6 O6
Query on GOL

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CA [auth I],
FA [auth K],
Q [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.48 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: H 3
  • Diffraction Data: https://doi.org/10.18430/M35US1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 340.17α = 90
b = 340.17β = 90
c = 62.77γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHENIXmodel 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)United StatesHHSCN27220120026C

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description