7MQK

AAC(3)-IIIa in complex with CoA and sisomicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted SISClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa.

Zielinski, M.Blanchet, J.Hailemariam, S.Berghuis, A.M.

(2022) PLoS One 17: e0269684-e0269684

  • DOI: https://doi.org/10.1371/journal.pone.0269684
  • Primary Citation of Related Structures:  
    7MQK, 7MQL, 7MQM

  • PubMed Abstract: 

    Canonical aminoglycosides are a large group of antibiotics, where the part of chemical diversity stems from the substitution of the neamine ring system on positions 5 and 6. Certain aminoglycoside modifying enzymes can modify a broad range of 4,5- and 4,6-disubstituted aminoglycosides, with some as many as 15. This study presents the structural and kinetic results describing a promiscuous aminoglycoside acetyltransferase AAC(3)-IIIa. This enzyme has been crystallized in ternary complex with coenzyme A and 4,5- and 4,6-disubstituted aminoglycosides. We have followed up this work with kinetic characterization utilizing a panel of diverse aminoglycosides, including a next-generation aminoglycoside, plazomicin. Lastly, we observed an alternative binding mode of gentamicin in the aminoglycoside binding site, which was proven to be a crystallographic artifact based on mutagenesis.


  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferase III
A, B, C, D
274Pseudomonas aeruginosaMutation(s): 0 
Gene Names: aacC3
EC: 2.3.1.81
UniProt
Find proteins for P29808 (Pseudomonas aeruginosa)
Explore P29808 
Go to UniProtKB:  P29808
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29808
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth C],
M [auth D]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SIS (Subject of Investigation/LOI)
Query on SIS

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth 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
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.175α = 90
b = 90.927β = 90
c = 100.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted SISClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-10-23
    Changes: Structure summary