Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 93.08 kDa 
• Atom Count: 6,696 
• Modelled Residue Count: 778 
• Deposited Residue Count: 830 
• Unique protein chains: 1

 2IYF

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

• PDB DOI:  https://doi.org/10.2210/pdb2IYF/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-07-17 Released: 2007-03-27 
• Deposition Author(s): 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.

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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 

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

• PubMed: 17376874 
• DOI: https://doi.org/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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OLEANDOMYCIN GLYCOSYLTRANSFERASE	A, B	415	Streptomyces antibioticus	Mutation(s): 0  Gene Names: oleD, UGT102A2 EC: 2.4.1
UniProt
Find proteins for Q53685 (Streptomyces antibioticus) Explore Q53685  Go to UniProtKB:  Q53685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ERY	C [auth A], E [auth B]	ERYTHROMYCIN A C37 H67 N O13 ULGZDMOVFRHVEP-RWJQBGPGSA-N
UDP	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ERY	PDBBind:  2IYF	Ki: 1.77e+5 (nM) from 1 assay(s)

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 = 72.718	α = 90
b = 65.778	β = 100.42
c = 91.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): 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.

Revision History  

• 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