3SWD

E. coli MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys115


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3ISS


Literature

Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA).

Zhu, J.Y.Yang, Y.Han, H.Betzi, S.Olesen, S.H.Marsilio, F.Schonbrunn, E.

(2012) J Biol Chem 287: 12657-12667

  • DOI: 10.1074/jbc.M112.342725
  • Primary Citation of Related Structures:  
    3SPB, 3SU9, 3SWQ, 3SWG, 3SWI, 3SWA, 3SWD, 3SWE, 3V4T, 3V5V

  • PubMed Abstract: 
  • The enzyme MurA has been an established antibiotic target since the discovery of fosfomycin, which specifically inhibits MurA by covalent modification of the active site residue Cys-115. Early biochemical studies established that Cys-115 also covalently reacts with substrate phosphoenolpyruvate (PEP) to yield a phospholactoyl adduct, but the structural and functional consequences of this reaction remained obscure ...

    The enzyme MurA has been an established antibiotic target since the discovery of fosfomycin, which specifically inhibits MurA by covalent modification of the active site residue Cys-115. Early biochemical studies established that Cys-115 also covalently reacts with substrate phosphoenolpyruvate (PEP) to yield a phospholactoyl adduct, but the structural and functional consequences of this reaction remained obscure. We captured and depicted the Cys-115-PEP adduct of Enterobacter cloacae MurA in various reaction states by X-ray crystallography. The data suggest that cellular MurA predominantly exists in a tightly locked complex with UDP-N-acetylmuramic acid (UNAM), the product of the MurB reaction, with PEP covalently attached to Cys-115. The uniqueness and rigidity of this "dormant" complex was previously not recognized and presumably accounts for the failure of drug discovery efforts toward the identification of novel and effective MurA inhibitors. We demonstrate that recently published crystal structures of MurA from various organisms determined by different laboratories were indeed misinterpreted and actually contain UNAM and covalently bound PEP. The Cys-115-PEP adduct was also captured in vitro during the reaction of free MurA and substrate UDP-N-acetylglucosamine or isomer UDP-N-acetylgalactosamine. The now available series of crystal structures allows a comprehensive view of the reaction cycle of MurA. It appears that the covalent reaction of MurA with PEP fulfills dual functions by tightening the complex with UNAM for the efficient feedback regulation of murein biosynthesis and by priming the PEP molecule for instantaneous reaction with substrate UDP-N-acetylglucosamine.


    Related Citations: 
    • Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .
      Jackson, S.G., Zhang, F., Chindemi, P., Junop, M.S., Berti, P.J.
      (2009) Biochemistry 48: 11715

    Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 1-carboxyvinyltransferaseABCDEFGHABCDEFGHIJKL
418Escherichia coli K-12Mutation(s): 1 
Gene Names: b3189JW3156murAmurZ
EC: 2.5.1.7
Find proteins for P0A749 (Escherichia coli (strain K12))
Explore P0A749 
Go to UniProtKB:  P0A749
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPZ
Query on EPZ

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid
C20 H31 N3 O19 P2
NQBRVZNDBBMBLJ-MQTLHLSBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
QPA
Query on QPA
A,B,C,D,E,F,G,H,I,J,K,LL-PEPTIDE LINKINGC6 H12 N O8 P SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.51α = 111.52
b = 120.91β = 104.44
c = 139.73γ = 90.19
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Other
  • Version 1.2: 2012-05-02
    Changes: Database references