6BBZ

Room temperature neutron/X-ray structure of sisomicin bound AAC-VIa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad.

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

(2018) Sci Adv 4: eaas8667-eaas8667

  • DOI: 10.1126/sciadv.aas8667
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related N -acetyltransferase (GNAT) superfamily. We show how a unique GNAT subfamily member uses a previously unidenti ...

    One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related N -acetyltransferase (GNAT) superfamily. We show how a unique GNAT subfamily member uses a previously unidentified noncanonical catalytic triad, consisting of a glutamic acid, a histidine, and the antibiotic substrate itself, which acts as a nucleophile and attacks the acetyl donor molecule. Neutron diffraction studies allow for unambiguous identification of a low-barrier hydrogen bond, predicted in canonical catalytic triads to increase basicity of the histidine. This work highlights the role of this unique catalytic triad in mediating antibiotic resistance while providing new insights into the design of the next generation of aminoglycosides.


    Organizational Affiliation

    Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AAC 3-VI protein
A
302Enterobacter cloacaeMutation(s): 0 
Gene Names: aac 3-VI
EC: 2.3.1.81
Find proteins for Q47030 (Enterobacter cloacae)
Go to UniProtKB:  Q47030
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIS
Query on SIS

Download CCD File 
A
(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: I 1 2 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.822α = 90
b = 86.169β = 94.55
c = 76.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-10-20 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Cuneo, M.J., Kumar, P.

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references