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: 1.768 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/acsinfecdis.6b00058
  • Primary Citation of Related Structures:  4E8O, 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-negati ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside N(6')-acetyltransferase type 1
A, B
166Acinetobacter haemolyticusEC: 2.3.1.82
Find proteins for Q44057 (Acinetobacter haemolyticus)
Go to UniProtKB:  Q44057
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TOY
Query on TOY

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Download CCD File 
A, B
TOBRAMYCIN
4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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
PHENIXrefinement
PHENIXmodel building
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references
  • Version 1.2: 2017-02-22
    Type: Database references