Macrolide 2'-phosphotransferase type II - complex with GDP and azithromycin

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.

Fong, D.H.Burk, D.L.Blanchet, J.Yan, A.Y.Berghuis, A.M.

(2017) Structure 25: 750-761.e5

  • DOI: https://doi.org/10.1016/j.str.2017.03.007
  • Primary Citation of Related Structures:  
    5IGH, 5IGI, 5IGJ, 5IGP, 5IGR, 5IGS, 5IGT, 5IGU, 5IGV, 5IGW, 5IGY, 5IGZ, 5IH0, 5IH1, 5IWU

  • PubMed Abstract: 

    The macrolides are a class of antibiotic, characterized by a large macrocyclic lactone ring that can be inactivated by macrolide phosphotransferase enzymes. We present structures for MPH(2')-I and MPH(2')-II in the apo state, and in complex with GTP analogs and six different macrolides. These represent the first structures from the two main classes of macrolide phosphotransferases. The structures show that the enzymes are related to the aminoglycoside phosphotransferases, but are distinguished from them by the presence of a large interdomain linker that contributes to an expanded antibiotic binding pocket. This pocket is largely hydrophobic, with a negatively charged patch located at a conserved aspartate residue, rationalizing the broad-spectrum resistance conferred by the enzymes. Complementary mutation studies provide insights into factors governing substrate specificity. A comparison with macrolides bound to their natural target, the 50S ribosome, suggests avenues for next-generation antibiotic development.

  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC H3G 0B1, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrolide 2'-phosphotransferase II302Escherichia coliMutation(s): 0 
Gene Names: mphBpO103_99
Find proteins for O32553 (Escherichia coli)
Explore O32553 
Go to UniProtKB:  O32553
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32553
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.23α = 90
b = 80.45β = 90
c = 96.43γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-13107

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description