4QC6

Crystal structure of aminoglycoside 6'-acetyltransferase-Ie


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 30NClick on this verticalbar to view detailsBest fitted KANClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis.

Smith, C.A.Toth, M.Weiss, T.M.Frase, H.Vakulenko, S.B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2754-2764

  • DOI: https://doi.org/10.1107/S1399004714017635
  • Primary Citation of Related Structures:  
    4QC6

  • PubMed Abstract: 

    Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.


  • Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional AAC/APH
A, B
179Staphylococcus warneriMutation(s): 0 
Gene Names: aacA-aphD
EC: 2.3.1 (PDB Primary Data), 2.7.1 (PDB Primary Data)
UniProt
Find proteins for Q7ATH7 (Staphylococcus warneri)
Explore Q7ATH7 
Go to UniProtKB:  Q7ATH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ATH7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
30N
Query on 30N

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
(3R,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3,5-diphosphaheptadecane-17-sulfinic acid 3,5-dioxide (non-preferred name)
C21 H36 N7 O18 P3 S
HHNOQZRCHLIIMA-IBOSZNHHSA-N
KAN
Query on KAN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.83α = 90
b = 89.72β = 90
c = 96.96γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 30NClick on this verticalbar to view detailsBest fitted KANClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations