6MB5

AAC-IIIb binary with NEOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Encoding of promiscuity in an aminoglycoside acetyltransferase.

Kumar, P.Selvaraj, B.Serpersu, E.H.Cuneo, M.J.

(2018) J. Med. Chem. --: --

  • DOI: 10.1021/acs.jmedchem.8b01393
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoglycoside antibiotics are a large family of antibiotics that can be divided into two distinct classes on the basis of the substitution pattern of the central deoxystreptamine ring. Although aminoglycosides are chemically, structurally, and topol ...

    Aminoglycoside antibiotics are a large family of antibiotics that can be divided into two distinct classes on the basis of the substitution pattern of the central deoxystreptamine ring. Although aminoglycosides are chemically, structurally, and topologically diverse, some aminoglycoside-modifying enzymes (AGMEs) are able to inactivate as many as 15 aminoglycosides from the two main classes, the kanamycin- and neomycin-based antibiotics. Here, we present the crystal structure of a promiscuous AGME, aminoglycoside- N3-acetyltransferase-IIIb (AAC-IIIb), in the apo form, in binary drug (sisomicin, neomycin, and paromomycin) and coenzyme A (CoASH) complexes, and in the ternary neomycin-CoASH complex. These data provide a structural framework for interpretation of the thermodynamics of enzyme-ligand interactions and the role of solvent in the recognition of ligands. In combination with the recent structure of an AGME that does not have broad substrate specificity, these structures allow for the direct determination of how antibiotic promiscuity is encoded in some AGMEs.


    Organizational Affiliation

    Graduate School of Genome Science and Technology , The University of Tennessee and Oak Ridge National Laboratory , 1414 West Cumberland Avenue , Knoxville , Tennessee 37996 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aac(3)-IIIb protein
A
274Pseudomonas aeruginosaMutation(s): 0 
Gene Names: aac(3)-IIIb
EC: 2.3.1.81
Find proteins for Q51405 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q51405
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY

Download SDF File 
Download CCD File 
A
NEOMYCIN
MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.245 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.120α = 90.00
b = 106.120β = 90.00
c = 68.970γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-08-29 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Cuneo, M.J., Kumar, P.

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release