5CFU

Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Revisiting the Catalytic Cycle and Kinetic Mechanism of AminoglycosideO-Nucleotidyltransferase(2′′): A Structural and Kinetic Study.

Bassenden, A.V.Park, J.Rodionov, D.Berghuis, A.M.

(2020) ACS Chem Biol 

  • DOI: 10.1021/acschembio.9b00904
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Aminoglycoside antibiotics have lost much of their effectiveness due to widespread resistance, primarily via covalent modification. One of the most ubiquitous enzymes responsible for aminoglycoside resistance is aminoglycoside O -nucleotidylt ...

    Aminoglycoside antibiotics have lost much of their effectiveness due to widespread resistance, primarily via covalent modification. One of the most ubiquitous enzymes responsible for aminoglycoside resistance is aminoglycoside O -nucleotidyltransferase(2″), which catalyzes a nucleotidylation reaction. Due to its clinical importance, much research has focused on dissecting the mechanism of action, some of it dating back more than 30 years. Here, we present structural data for catalytically informative states of the enzyme, i.e., ANT(2″) in complex with adenosine monophosphate (AMP) and tobramycin (inactive-intermediate state) and in complex with adenylyl-2″-tobramycin, pyrophosphate, and Mn 2+ (product-bound state). These two structures in conjunction with our previously reported structure of ANT(2″)'s substrate-bound complex capture clinical states along ANT(2″)'s reaction coordinate. Additionally, isothermal titration calorimetry (ITC)-based studies are presented that assess the order of substrate binding and product release. Combined, these results outline a kinetic mechanism for ANT(2″) that contradicts what has been previously reported. Specifically, we show that the release of adenylated aminoglycoside precedes pyrophosphate. Furthermore, the ternary complex structures provide additional details on the catalytic mechanism, which reveals extensive similarities to the evolutionarily related DNA polymerase-β superfamily.


    Organizational Affiliation

    Centre de Recherche en Biologie Structurale, McGill University, Bellini Life Science Complex, 3649 Promenade Sir William Osler, Montréal, Québec Canada, H3G 0B1.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside Nucleotidyltransferase (2")-Ia
A
185Pseudomonas aeruginosaMutation(s): 0 
Gene Names: aadBTNCP6
Find proteins for Q6X3H6 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q6X3H6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
51H
Query on 51H

Download CCD File 
A
adenylyl-2"-tobramycin
C28 H49 N10 O15 P
RHQLHNATZATWNZ-XMUWNKPOSA-N
 Ligand Interaction
POP
Query on POP

Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
BU1
Query on BU1

Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.09α = 90
b = 41.91β = 105.08
c = 47.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
StructureStudiodata collection
xia2data scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaCIHR MOP-13107

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2020-03-18
    Changes: Database references