3TDV

Structure of the GDP complex of wild-type aminoglycoside 2'-phosphotransferase-IIIa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Aminoglycoside-2' phosphotransferase-IIIa (APH(2')-IIIa) prefers GTP over ATP: Structural templates for nucleotide recognition in the bacterial aminoglycoside-2' kinases.

Smith, C.A., Toth, M., Frase, H., Byrnes, L.J., Vakulenko, S.B.

(2012) J.Biol.Chem. 287: 12893-12903

  • DOI: 10.1074/jbc.M112.341206
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Contrary to the accepted dogma that ATP is the canonical phosphate donor in aminoglycoside kinases and protein kinases, it was recently demonstrated that all members of the bacterial aminoglycoside 2''-phosphotransferase IIIa (APH(2'')) aminoglycosid ...

    Contrary to the accepted dogma that ATP is the canonical phosphate donor in aminoglycoside kinases and protein kinases, it was recently demonstrated that all members of the bacterial aminoglycoside 2''-phosphotransferase IIIa (APH(2'')) aminoglycoside kinase family are unique in their ability to utilize GTP as a cofactor for antibiotic modification. Here we describe the structural determinants for GTP recognition in these enzymes. The crystal structure of the GTP-dependent APH(2'')-IIIa shows that although this enzyme has templates for both ATP and GTP binding superimposed on a single nucleotide specificity motif, access to the ATP-binding template is blocked by a bulky tyrosine residue. Substitution of this tyrosine by a smaller amino acid opens access to the ATP template. Similar GTP binding templates are conserved in other bacterial aminoglycoside kinases, whereas in the structurally related eukaryotic protein kinases this template is less conserved. The aminoglycoside kinases are important antibiotic resistance enzymes in bacteria, whose wide dissemination severely limits available therapeutic options, and the GTP binding templates could be exploited as new, previously unexplored targets for inhibitors of these clinically important enzymes.

    Organizational Affiliation: 

    Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025, USA. csmith@slac.stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gentamicin resistance protein
A, B
306Enterococcus gallinarumMutation(s): 0 
Find proteins for P96762 (Enterococcus gallinarum)
Go to UniProtKB:  P96762
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.680α = 89.94
b = 54.650β = 103.83
c = 77.160γ = 106.84
Software Package:
Software NamePurpose
Blu-Icedata collection
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-14
    Type: Database references
  • Version 1.2: 2012-05-02
    Type: Database references
  • Version 1.3: 2020-02-26
    Type: Data collection