3I0Q

Crystal Structure of the AMP-bound complex of Spectinomycin Phosphotransferase, APH(9)-Ia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila.

Fong, D.H.Lemke, C.T.Hwang, J.Xiong, B.Berghuis, A.M.

(2010) J.Biol.Chem. 285: 9545-9555

  • DOI: 10.1074/jbc.M109.038364
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoglycoside phosphotransferases (APHs) constitute a diverse group of enzymes that are often the underlying cause of aminoglycoside resistance in the clinical setting. Several APHs have been extensively characterized, including the elucidation of t ...

    Aminoglycoside phosphotransferases (APHs) constitute a diverse group of enzymes that are often the underlying cause of aminoglycoside resistance in the clinical setting. Several APHs have been extensively characterized, including the elucidation of the three-dimensional structure of two APH(3') isozymes and an APH(2'') enzyme. Although many APHs are plasmid-encoded and are capable of inactivating numerous 2-deoxystreptmaine aminoglycosides with multiple regiospecificity, APH(9)-Ia, isolated from Legionella pneumophila, is an unusual enzyme among the APH family for its chromosomal origin and its specificity for a single non-2-deoxystreptamine aminoglycoside substrate, spectinomycin. We describe here the crystal structures of APH(9)-Ia in its apo form, its binary complex with the nucleotide, AMP, and its ternary complex bound with ADP and spectinomycin. The structures reveal that APH(9)-Ia adopts the bilobal protein kinase-fold, analogous to the APH(3') and APH(2'') enzymes. However, APH(9)-Ia differs significantly from the other two types of APH enzymes in its substrate binding area and that it undergoes a conformation change upon ligand binding. Moreover, kinetic assay experiments indicate that APH(9)-Ia has stringent substrate specificity as it is unable to phosphorylate substrates of choline kinase or methylthioribose kinase despite high structural resemblance. The crystal structures of APH(9)-Ia demonstrate and expand our understanding of the diversity of the APH family, which in turn will facilitate the development of new antibiotics and inhibitors.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spectinomycin phosphotransferase
A
339Legionella pneumophilaMutation(s): 0 
Gene Names: aph
Find proteins for O06916 (Legionella pneumophila)
Go to UniProtKB:  O06916
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.262 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.466α = 90.00
b = 74.466β = 90.00
c = 135.526γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance