5UXD

Crystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium in complex with azithromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The evolution of substrate discrimination in macrolide antibiotic resistance enzymes.

Pawlowski, A.C.Stogios, P.J.Koteva, K.Skarina, T.Evdokimova, E.Savchenko, A.Wright, G.D.

(2018) Nat Commun 9: 112-112

  • DOI: 10.1038/s41467-017-02680-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The production of antibiotics by microbes in the environment and their use in medicine and agriculture select for existing and emerging resistance. To address this inevitability, prudent development of antibiotic drugs requires careful consideration ...

    The production of antibiotics by microbes in the environment and their use in medicine and agriculture select for existing and emerging resistance. To address this inevitability, prudent development of antibiotic drugs requires careful consideration of resistance evolution. Here, we identify the molecular basis for expanded substrate specificity in MphI, a macrolide kinase (Mph) that does not confer resistance to erythromycin, in contrast to other known Mphs. Using a combination of phylogenetics, drug-resistance phenotypes, and in vitro enzyme assays, we find that MphI and MphK phosphorylate erythromycin poorly resulting in an antibiotic-sensitive phenotype. Using likelihood reconstruction of ancestral sequences and site-saturation combinatorial mutagenesis, supported by Mph crystal structures, we determine that two non-obvious mutations in combination expand the substrate range. This approach should be applicable for studying the functional evolution of any antibiotic resistance enzyme and for evaluating the evolvability of resistance enzymes to new generations of antibiotic scaffolds.


    Organizational Affiliation

    Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8S 4L8, ON, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrolide 2'-phosphotransferase MphH
A, B
300Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / NCIB 9860)Mutation(s): 0 
Find proteins for C7MEP1 (Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / NCIB 9860))
Go to UniProtKB:  C7MEP1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ZIT
Query on ZIT

Download SDF File 
Download CCD File 
A, B
AZITHROMYCIN
C38 H72 N2 O12
MQTOSJVFKKJCRP-BICOPXKESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 55.050α = 90.00
b = 81.210β = 96.83
c = 71.340γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesHHSCN27220120026C

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 2.0: 2018-02-21
    Type: Database references, Polymer sequence