3I0Q | pdb_00003i0q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.346 (Depositor), 0.344 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

Starting Model: experimental
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This is version 1.2 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 Biological Chem 285: 9545-9555

  • DOI: https://doi.org/10.1074/jbc.M109.038364
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 40.05 kDa 
  • Atom Count: 2,634 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 339 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spectinomycin phosphotransferase339Legionella pneumophila serogroup 1Mutation(s): 0 
Gene Names: aphaph9
UniProt
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
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.346 (Depositor), 0.344 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.466α = 90
b = 74.466β = 90
c = 135.526γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description