3VCY

Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase), from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin.

• PDB DOI: https://doi.org/10.2210/pdb3VCY/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Aliivibrio fischeri MJ11
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-04 Released: 2012-04-11 
• Deposition Author(s): Bensen, D.C., Rodriguez, S., Nix, J., Cunningham, M.L., Tari, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin.

Bensen, D.C., Rodriguez, S., Nix, J., Cunningham, M.L., Tari, L.W.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 382-385

• PubMed: 22505403 
• DOI: https://doi.org/10.1107/S1744309112006720
• Primary Citation of Related Structures:  
  3VCY


• PubMed Abstract: 
  

  The development of new antibiotics is necessitated by the rapid development of resistance to current therapies. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), which catalyzes the first committed step of bacterial peptidoglycan biosynthesis, is a prime candidate for therapeutic intervention. MurA is the target of the antibiotic fosfomycin, a natural product produced by Streptomyces. Despite possessing a high degree of sequence conservation with MurA enzymes from fosfomycin-susceptible organisms, recent microbiological studies suggest that MurA from Vibrio fischeri (VfiMurA) may confer fosfomycin resistance via a mechanism that is not yet understood. The crystal structure of VfiMurA in a ternary complex with the substrate UDP-N-acetylglucosamine (UNAG) and fosfomycin has been solved to a resolution of 1.93 Å. Fosfomycin is known to inhibit MurA by covalently binding to a highly conserved cysteine in the active site of the enzyme. A comparison of the title structure with the structure of fosfomycin-susceptible Haemophilus influenzae MurA (PDB entry 2rl2) revealed strikingly similar conformations of the mobile substrate-binding loop and clear electron density for a fosfomycin-cysteine adduct. Based on these results, there are no distinguishing sequence/structural features in VfiMurA that would translate to a diminished sensitivity to fosfomycin. However, VfiMurA is a robust crystallizer and shares high sequence identity with many clinically relevant bacterial pathogens. Thus, it would serve as an ideal system for use in the structure-guided optimization of new antibacterial agents.

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Organizational Affiliation: 

Structural Biology, Trius Therapeutics, 6310 Nancy Ridge Drive, Suite 101, San Diego, CA 92008, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 186.94 kDa 
• Atom Count: 13,938 
• Modelled Residue Count: 1,676 
• Deposited Residue Count: 1,720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B, C, D	430	Aliivibrio fischeri MJ11	Mutation(s): 0  Gene Names: murA, VFMJ11_0391 EC: 2.5.1.7
UniProt
Find proteins for B5F9P4 (Aliivibrio fischeri (strain MJ11)) Explore B5F9P4  Go to UniProtKB:  B5F9P4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1	F [auth A], I [auth B], M [auth C], Q [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N
FFQ	E [auth A], J [auth B], O [auth C], T [auth D]	[(1R)-1-hydroxypropyl]phosphonic acid C3 H9 O4 P MVIJUJBSAAUHEM-GSVOUGTGSA-N
PO4	G [auth A], K [auth B], N [auth C], R [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth A], L [auth B], P [auth C], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.6	α = 90
b = 118.51	β = 116.48
c = 92.51	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Bensen, D.C., Rodriguez, S., Nix, J., Cunningham, M.L., Tari, L.W.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary