Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.92 kDa 
• Atom Count: 2666 
• Modelled Residue Count: 292 
• Deposited Residue Count: 332 
• Unique protein chains: 1

4EVY

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

• PDB DOI: 10.2210/pdb4EVY/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Acinetobacter haemolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2012-05-09 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Minasov, G., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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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 

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

• PubMed: 27785912 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(6')-acetyltransferase type 1	A, B	166	Acinetobacter haemolyticus	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOY	C [auth A], G [auth B]	TOBRAMYCIN C18 H37 N5 O9 NLVFBUXFDBBNBW-PBSUHMDJSA-N
K	D [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	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 DOI: 10.18430/M34EVY Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.723	α = 83.65
b = 43.789	β = 87.49
c = 46.282	γ = 68.41

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-26 
• Released Date: 2012-05-09 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Minasov, G., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• 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