Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 32.84 kDa 
• Atom Count: 2131 
• Modelled Residue Count: 268 
• Deposited Residue Count: 302 
• Unique protein chains: 1

6NTI

Neutron/X-ray crystal structure of AAC-VIa bound to kanamycin b

• PDB DOI: 10.2210/pdb6NTI/pdb

• Classification: transferase/antibiotic
• Organism(s): Enterobacteriaceae
• Expression System: Escherichia coli DH1
• Mutation(s): No 


• Deposited: 2019-01-29 Released: 2019-09-25 
• Deposition Author(s): Cuneo, M.J., Kumar, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 

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• Method: NEUTRON DIFFRACTION

Literature

Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.

Kumar, P., Agarwal, P.K., Waddell, M.B., Mittag, T., Serpersu, E.H., Cuneo, M.J.

(2019) Angew Chem Int Ed Engl 58: 16260-16266

• PubMed: 31515870 
• DOI: 10.1002/anie.201908535
• Primary Citation of Related Structures:  
  6NP1, 6NP2, 6NP3, 6NP4, 6NP5, 6NTI, 6NTJ, 6O5U


• PubMed Abstract: 
  

The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.

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Organizational Affiliation: 

Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(3)-acetyltransferase	A	302	Enterobacteriaceae	Mutation(s): 0  Gene Names: aacC, aac3-VI, aac3-VI_1, NCTC13462_00209, pAPEC1990_61_126, pAR060302_0140, pAR060302_133, peH4H_0115, SAMEA3485113_05325 EC: 2.3.1.81
UniProt
Find proteins for C4NV15 (Escherichia coli) Explore C4NV15  Go to UniProtKB:  C4NV15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9CS	B [auth A]	(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE C18 H37 N5 O10 SKKLOUVUUNMCJE-FQSMHNGLSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 
• Space Group: I 1 2 1

• Method: NEUTRON DIFFRACTION
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.359	α = 90
b = 86.058	β = 93.98
c = 77.597	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-29 
• Released Date: 2019-09-25 
Deposition Author(s): Cuneo, M.J., Kumar, P.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references