Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 23.76 kDa 
• Atom Count: 1644 
• Residue Count: 176 
• Unique protein chains: 1

1V0C

Structure of AAC(6')-Ib in complex with Kanamycin C and AcetylCoA.

• DOI: 10.2210/pdb1V0C/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-03-20 Released: 2008-09-02 
• Deposition Author(s): Vetting, M.W., Park, C.H., Hedge, S.S., Hooper, D.C., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Mechanistic and Structural Analysis of Aminoglycoside N-Acetyltransferase Aac(6')-Ib and its Bifunctional, Fluoroquinolone-Active Aac(6')-Ib-Cr Variant.

Vetting, M.W., Park, C.H., Hegde, S.S., Jacoby, G.A., Hooper, D.C., Blanchard, J.S.

(2008) Biochemistry 47: 9825

• PubMed: 18710261 
• DOI: 10.1021/bi800664x
• Primary Citation of Related Structures:  
  2BUE, 2VQY, 1V0C


• PubMed Abstract: 
  

Enzymatic modification of aminoglycoside antibiotics mediated by regioselective aminoglycoside N-acetyltransferases is the predominant cause of bacterial resistance to aminoglycosides. A recently discovered bifunctional aminoglycoside acetyltransferase (AAC(6')-Ib variant, AAC(6')-Ib-cr) has been shown to catalyze the acetylation of fluoroquinolones as well as aminoglycosides. We have expressed and purified AAC(6')-Ib-wt and its bifunctional variant AAC(6')-Ib-cr in Escherichia coli and characterized their kinetic and chemical mechanism. Initial velocity and dead-end inhibition studies support an ordered sequential mechanism for the enzyme(s). The three-dimensional structure of AAC(6')-Ib-wt was determined in various complexes with donor and acceptor ligands to resolutions greater than 2.2 A. Observation of the direct, and optimally positioned, interaction between the 6'-NH 2 and Asp115 suggests that Asp115 acts as a general base to accept a proton in the reaction. The structure of AAC(6')-Ib-wt permits the construction of a molecular model of the interactions of fluoroquinolones with the AAC(6')-Ib-cr variant. The model suggests that a major contribution to the fluoroquinolone acetylation activity comes from the Asp179Tyr mutation, where Tyr179 makes pi-stacking interactions with the quinolone ring facilitating quinolone binding. The model also suggests that fluoroquinolones and aminoglycosides have different binding modes. On the basis of kinetic properties, the pH dependence of the kinetic parameters, and structural information, we propose an acid/base-assisted reaction catalyzed by AAC(6')-Ib-wt and the AAC(6')-Ib-cr variant involving a ternary complex.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAC(6')-IB	A	202	Escherichia coli	Mutation(s): 2  Gene Names:  AAC(6')-Ib, aac(6')-Ib-cr, aac(6`)-Ib-cr, aacA, aacA-aphD, aacA-aphD_1, aacA-aphD_2, aacA4, aacA4-cr, AZ95_0017, B634_00009, BANRA_05200, BK248_28590, BVL39_26675, ECTO124_05278, ExPECSC065_03527, HmCms169_04570, pCTXM15_EC8_00014, pEcNDM0_00009, pHKU1_04, RCS105_pI0073, RCS57_p0092, RCS59_P0123, RCS67_P0023, SAMEA4370365_00001, SAMEA4370365_00042 EC: 2.3.1.82
Find proteins for Q6SJ71 (Escherichia coli) Explore Q6SJ71  Go to UniProtKB:  Q6SJ71

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	A	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
KNC	A	KANAMYCIN C C18 H36 N4 O11 WZDRWYJKESFZMB-FQSMHNGLSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.399	α = 90
b = 57.399	β = 90
c = 147.113	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-20 
• Released Date: 2008-09-02 
Deposition Author(s): Vetting, M.W., Park, C.H., Hedge, S.S., Hooper, D.C., Blanchard, J.S.

Revision History 

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other