6BC7 | pdb_00006bc7

Cryo X-ray structure of sisomicin bound AAC-VIa

• PDB DOI: https://doi.org/10.2210/pdb6BC7/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

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

• PubMed: 29632894 
• DOI: https://doi.org/10.1126/sciadv.aas8667
• Primary Citation Related Structures: 
  6BBR, 6BBZ, 6BC2, 6BC3, 6BC4, 6BC5, 6BC6, 6BC7


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

Biological Assembly 1  

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 32.85 kDa 
• Atom Count: 2,526 
• Modeled Residue Count: 268 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAC 3-VI protein	A	302	Enterobacter cloacae	Mutation(s): 0  Gene Names: aac 3-VI EC: 2.3.1
UniProt
Find proteins for Q47030 (Enterobacter cloacae) Explore Q47030  Go to UniProtKB:  Q47030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIS	B [auth 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
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.55	α = 90
b = 78.55	β = 90
c = 83.604	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description