2PR8 | pdb_00002pr8

crystal structure of aminoglycoside N-acetyltransferase AAC(6')-Ib11

• PDB DOI: https://doi.org/10.2210/pdb2PR8/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-04 Released: 2008-04-08 
• Deposition Author(s): Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E., Dardel, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.252 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance.

Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E., Dardel, F.

(2008) EMBO Rep 9: 344-349

• PubMed: 18292754 
• DOI: https://doi.org/10.1038/embor.2008.9
• Primary Citation Related Structures: 
  2PR8, 2PRB, 2QIR


• PubMed Abstract: 
  

  The emergence of multi-resistant pathogenic bacteria is a worldwide health issue. Recently, clinical variants of a single antibiotic-modifying acetyltransferase, AAC(6')-Ib-a variant of aminoglycoside 6'-N-acetyltransferase-have been identified that confer extended resistance to most aminoglycosides and, more surprisingly, to structurally unrelated fluoroquinolones. The corresponding gene is carried by mobile genetic elements and is present in most multi-resistant pathogenic strains, hence making it a serious threat to current therapies. Here, we report the crystal structures of both narrow- and broad-spectrum resistance variants of this enzyme, which reveal the structural basis for the emergence of extended resistance. The active site shows an important plasticity and has adapted to new substrates by a large-scale gaping process. We have also obtained co-crystals with both substrates, and with a simple transition state analogue, which provides new clues for the design of inhibitors of this resistance mechanism.

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Organizational Affiliation: 
• Cristallographie and RMN Biologiques, Université Paris Descartes, CNRS, 4 Avenue de l'Observatoire, 75006 Paris, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.24 kDa 
• Atom Count: 2,935 
• Modeled Residue Count: 346 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside 6-N-acetyltransferase type Ib11	A, B	196	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  EC: 2.3.1.82
UniProt
Find proteins for Q8GLI5 (Salmonella typhimurium) Explore Q8GLI5  Go to UniProtKB:  Q8GLI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A], D [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.62	α = 90
b = 85.37	β = 90
c = 150.41	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Maurice, F., Broutin, I., Podglajen, I., Benas, P., Collatz, E., Dardel, F.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations