5US1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

  • 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 prod ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside 2'-N-acetyltransferaseABCDEFGHIJKL189Providencia stuartiiMutation(s): 0 
Gene Names: aac
EC: 2.3.1.59
Find proteins for Q52424 (Providencia stuartii)
Explore Q52424 
Go to UniProtKB:  Q52424
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download CCD File 
C
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
COA
Query on COA

Download CCD File 
E, I, L
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
8MM
Query on 8MM

Download CCD File 
A, B, D, E, F, G, H, I, K, L
(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
RLGSXXMFPPOROB-JOYMZIHVSA-N
 Ligand Interaction
TAR
Query on TAR

Download CCD File 
A, D, F, H, J
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
C, I, K
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 DOI: 10.18430/M35US1 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 340.17α = 90
b = 340.17β = 90
c = 62.77γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building

Structure Validation

View Full Validation Report



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 

  • 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