2IYF

The crystal structure of macrolide glycosyltransferases: A blueprint for antibiotic engineering


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4M83


Literature

The Crystal Structure of Two Macrolide Glycosyltransferases Provides a Blueprint for Host Cell Antibiotic Immunity.

Bolam, D.N.Roberts, S.M.Proctor, M.R.Turkenburg, J.P.Dodson, E.J.Martinez-Fleites, C.Yang, M.Davis, B.G.Davies, G.J.Gilbert, H.J.

(2007) Proc Natl Acad Sci U S A 104: 5336

  • DOI: 10.1073/pnas.0607897104
  • Primary Citation of Related Structures:  
    2IYA, 2IYF

  • PubMed Abstract: 
  • Glycosylation of macrolide antibiotics confers host cell immunity from endogenous and exogenous agents. The Streptomyces antibioticus glycosyltransferases, OleI and OleD, glycosylate and inactivate oleandomycin and diverse macrolides including erythromycin, respectively ...

    Glycosylation of macrolide antibiotics confers host cell immunity from endogenous and exogenous agents. The Streptomyces antibioticus glycosyltransferases, OleI and OleD, glycosylate and inactivate oleandomycin and diverse macrolides including erythromycin, respectively. The structure of these enzyme-ligand complexes, in tandem with kinetic analysis of site-directed variants, provide insight into the interaction of macrolides with their synthetic apparatus. Erythromycin binds to OleD and the 23S RNA of its target ribosome in the same conformation and, although the antibiotic contains a large number of polar groups, its interaction with these macromolecules is primarily through hydrophobic contacts. Erythromycin and oleandomycin, when bound to OleD and OleI, respectively, adopt different conformations, reflecting a subtle effect on sugar positioning by virtue of a single change in the macrolide backbone. The data reported here provide structural insight into the mechanism of resistance to both endogenous and exogenous antibiotics, and will provide a platform for the future redesign of these catalysts for antibiotic remodelling.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OLEANDOMYCIN GLYCOSYLTRANSFERASEA, B415Streptomyces antibioticusMutation(s): 0 
Gene Names: oleDUGT102A2
EC: 2.4.1
Find proteins for Q53685 (Streptomyces antibioticus)
Explore Q53685 
Go to UniProtKB:  Q53685
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERY
Query on ERY

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ERYTHROMYCIN A
C37 H67 N O13
ULGZDMOVFRHVEP-RWJQBGPGSA-N
 Ligand Interaction
UDP
Query on UDP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ERYKi :  177300   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.718α = 90
b = 65.778β = 100.42
c = 91.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance