Crystal Structure of apo Spectinomycin Phosphotransferase, APH(9)-Ia

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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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: https://doi.org/10.1074/jbc.M109.038364
  • Primary Citation of Related Structures:  
    3I0O, 3I0Q, 3I1A

  • 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 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 H3G 1Y6; Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada. Electronic address: albert.berghuis@mcgill.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spectinomycin phosphotransferase
A, B
339Legionella pneumophila serogroup 1Mutation(s): 0 
Gene Names: aphaph9
Find proteins for O06916 (Legionella pneumophila)
Explore O06916 
Go to UniProtKB:  O06916
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06916
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.41α = 90
b = 70.695β = 95.93
c = 99.307γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations