4EVY

Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-Ig from Acinetobacter haemolyticus in complex with tobramycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes.

Stogios, P.J.Kuhn, M.L.Evdokimova, E.Law, M.Courvalin, P.Savchenko, A.

(2017) ACS Infect Dis 3: 132-143

  • DOI: https://doi.org/10.1021/acsinfecdis.6b00058
  • Primary Citation of Related Structures:  
    4E8O, 4EVY, 4F0Y

  • PubMed Abstract: 

    Modification of aminoglycosides by N-acetyltransferases (AACs) is one of the major mechanisms of resistance to these antibiotics in human bacterial pathogens. More than 50 enzymes belonging to the AAC(6') subfamily have been identified in Gram-negative and Gram-positive clinical isolates. Our understanding of the molecular function and evolutionary origin of these resistance enzymes remains incomplete. Here we report the structural and enzymatic characterization of AAC(6')-Ig and AAC(6')-Ih from Acinetobacter spp. The crystal structure of AAC(6')-Ig in complex with tobramycin revealed a large substrate-binding cleft remaining partially unoccupied by the substrate, which is in stark contrast with the previously characterized AAC(6')-Ib enzyme. Enzymatic analysis indicated that AAC(6')-Ig and -Ih possess a broad specificity against aminoglycosides but with significantly lower turnover rates as compared to other AAC(6') enzymes. Structure- and function-informed phylogenetic analysis of AAC(6') enzymes led to identification of at least three distinct subfamilies varying in oligomeric state, active site composition, and drug recognition mode. Our data support the concept of AAC(6') functionality originating through convergent evolution from diverse Gcn5-related-N-acetyltransferase (GNAT) ancestral enzymes, with AAC(6')-Ig and -Ih representing enzymes that may still retain ancestral nonresistance functions in the cell as provided by their particular active site properties.


  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario M5G 1L6, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N(6')-acetyltransferase type 1
A, B
166Acinetobacter haemolyticusMutation(s): 0 
Gene Names: aac(6')-Ig
EC: 2.3.1.82
UniProt
Find proteins for Q44057 (Acinetobacter haemolyticus)
Explore Q44057 
Go to UniProtKB:  Q44057
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ44057
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TOY
Query on TOY

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
TOBRAMYCIN
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/m34evy
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.723α = 83.65
b = 43.789β = 87.49
c = 46.282γ = 68.41
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description