6BC3

Cryo X-ray structure of sisomicin bound AAC-VIa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.047 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related <i>N </i>-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

    Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.,National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314, USA.,Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,University of Tennessee-Oak Ridge National Laboratory Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, 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
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
SIS
Query on SIS

Download SDF File 
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
Sisomicin
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.047 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.189 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 77.534α = 90.00
b = 77.534β = 90.00
c = 83.890γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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