7TB0

E. faecium MurAA in complex with fosfomycin and UNAG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.118 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Enolpyruvate transferase MurAA A149E , identified during adaptation of Enterococcus faecium to daptomycin, increases stability of MurAA-MurG interaction.

Zhou, Y.Utama, B.Pratap, S.Supandy, A.Song, X.Tran, T.T.Mehta, H.H.Arias, C.A.Shamoo, Y.

(2023) J Biol Chem 299: 102912-102912

  • DOI: https://doi.org/10.1016/j.jbc.2023.102912
  • Primary Citation of Related Structures:  
    7TB0

  • PubMed Abstract: 

    Daptomycin (DAP) is an antibiotic frequently used as a drug of last resort against vancomycin-resistant enterococci. One of the major challenges when using DAP against vancomycin-resistant enterococci is the emergence of resistance, which is mediated by the cell-envelope stress system LiaFSR. Indeed, inhibition of LiaFSR signaling has been suggested as a strategy to "resensitize" enterococci to DAP. In the absence of LiaFSR, alternative pathways mediating DAP resistance have been identified, including adaptive mutations in the enolpyruvate transferase MurAA (MurAA A149E ), which catalyzes the first committed step in peptidoglycan biosynthesis; however, how these mutations confer resistance is unclear. Here, we investigated the biochemical basis for MurAA A149E -mediated adaptation to DAP to determine whether such an alternative pathway would undermine the potential efficacy of therapies that target the LiaFSR pathway. We found cells expressing MurAA A149E had increased susceptibility to glycoside hydrolases, consistent with decreased cell wall integrity. Furthermore, structure-function studies of MurAA and MurAA A149E using X-ray crystallography and biochemical analyses indicated only a modest decrease in MurAA A149E activity, but a 16-fold increase in affinity for MurG, which performs the last intracellular step of peptidoglycan synthesis. Exposure to DAP leads to mislocalization of cell division proteins including MurG. In Bacillus subtilis, MurAA and MurG colocalize at division septa and, thus, we propose MurAA A149E may contribute to DAP nonsusceptibility by increasing the stability of MurAA-MurG interactions to reduce DAP-induced mislocalization of these essential protein complexes.


  • Organizational Affiliation

    Department of Biosciences, Rice University, Houston, Texas, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
A, B, C, D
433Enterococcus faeciumMutation(s): 0 
Gene Names: 
EC: 2.5.1.7
UniProt
Find proteins for A0A133CTP6 (Enterococcus faecium)
Explore A0A133CTP6 
Go to UniProtKB:  A0A133CTP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A133CTP6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD1 (Subject of Investigation/LOI)
Query on UD1

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
R [auth C],
X [auth D]
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
FFQ (Subject of Investigation/LOI)
Query on FFQ

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B],
S [auth C],
Y [auth D]
[(1R)-1-hydroxypropyl]phosphonic acid
C3 H9 O4 P
MVIJUJBSAAUHEM-GSVOUGTGSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
T [auth C],
U [auth C],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth D],
M [auth A],
Q [auth B],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D],
L [auth A],
V [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.118 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.03α = 115.06
b = 96.81β = 99.15
c = 96.821γ = 103.88
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 A1080714

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references, Refinement description
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-01-17
    Changes: Database references