9MH3 | pdb_00009mh3

Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with acetyl coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzyme-mediated aminoglycoside resistance without target mimicry.

Hemmings, M.Zielinski, M.Golkar, T.Blanchet, J.Pistofidis, A.Munro, K.Schmeing, T.M.Bohle, D.S.Berghuis, A.M.

(2025) Commun Chem 8: 258-258

  • DOI: https://doi.org/10.1038/s42004-025-01666-0
  • Primary Citation of Related Structures:  
    9MGS, 9MGT, 9MGU, 9MH3, 9MH5, 9MH6, 9MH7

  • PubMed Abstract: 

    The primary mode of resistance to aminoglycoside antibiotics is through chemical modification catalyzed by aminoglycoside-modifying enzymes. Numerous structural studies of these enzymes have invariably shown that they bind aminoglycosides in the same lowest-energy conformation as the intended target for these antibiotics, the A site of the bacterial ribosome. Presumably, the binding mode mimicry enables these enzymes to compete successfully with the target, thus conferring effective resistance. Here we present the first structural and functional studies of two aminoglycoside-modifying enzymes that do not use target mimicry, AAC(3)-Ia and AAC(3)-XIa. X-ray diffraction studies reveal that these enzymes bind aminoglycoside antibiotics in a conformation where the central 2-deoxystreptamine ring is in boat conformation. The effect of this non-canonical binding mode on the enzymes' ability to modify antibiotics is assessed in silico and in vitro, and its impact for conferring resistance is assessed in vivo. Overall, the results show that target mimicry, while advantageous, is not an essential strategy for aminoglycoside-modifying enzymes to be effective in conferring resistance.


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montréal, QC, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N-acetyltransferase AAC(3)-XI
A, B
148Corynebacterium striatumMutation(s): 0 
Gene Names: CBE89_03745
UniProt
Find proteins for A0A0K2X0F2 (Corynebacterium striatum)
Explore A0A0K2X0F2 
Go to UniProtKB:  A0A0K2X0F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K2X0F2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.422α = 90
b = 99.512β = 106.4
c = 39.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-162365

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references