Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.61 kDa 
• Atom Count: 4585 
• Modelled Residue Count: 587 
• Deposited Residue Count: 596 
• Unique protein chains: 1

5UXB

Crystal structure of macrolide 2'-phosphotransferase MphH from Brachybacterium faecium, apoenzyme

• PDB DOI: 10.2210/pdb5UXB/pdb

• Classification: TRANSFERASE
• Organism(s): Brachybacterium faecium DSM 4810
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-22 Released: 2017-07-26 
• Deposition Author(s): Stogios, P.J., Skarina, T., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

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

• PubMed: 29317655 
• DOI: 10.1038/s41467-017-02680-0
• Primary Citation of Related Structures:  
  5UXA, 5UXB, 5UXC, 5UXD


• 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 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.

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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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide 2'-phosphotransferase MphH	A, B	298	Brachybacterium faecium DSM 4810	Mutation(s): 0  Gene Names: Bfae_22410
UniProt
Find proteins for C7MEP1 (Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / JCM 11609 / LMG 19847 / NBRC 14762 / NCIMB 9860 / 6-10)) Explore C7MEP1  Go to UniProtKB:  C7MEP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.18430/M35UXB Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.933	α = 90
b = 79.741	β = 90
c = 99.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-22 
• Released Date: 2017-07-26 
Deposition Author(s): Stogios, P.J., Skarina, T., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSCN27220120026C

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 2.0: 2018-02-21
  Changes: Database references, Polymer sequence
• Version 2.1: 2019-12-11
  Changes: Author supporting evidence