5V2L

Mevalonate diphosphate mediated ATP binding mechanism of the mevalonate diphosphate decarboxylase from Enterococcus faecalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis.

Chen, C.L.Mermoud, J.C.Paul, L.N.Steussy, C.N.Stauffacher, C.V.

(2017) J. Biol. Chem. 292: 21340-21351

  • DOI: 10.1074/jbc.M117.802223
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mevalonate pathway produces isopentenyl diphosphate (IPP), a building block for polyisoprenoid synthesis, and is a crucial pathway for growth of the human bacterial pathogen <i>Enterococcus faecalis </i> The final enzyme in this pathway, mevalon ...

    The mevalonate pathway produces isopentenyl diphosphate (IPP), a building block for polyisoprenoid synthesis, and is a crucial pathway for growth of the human bacterial pathogen Enterococcus faecalis The final enzyme in this pathway, mevalonate diphosphate decarboxylase (MDD), acts on mevalonate diphosphate (MVAPP) to produce IPP while consuming ATP. This essential enzyme has been suggested as a therapeutic target for the treatment of drug-resistant bacterial infections. Here, we report functional and structural studies on the mevalonate diphosphate decarboxylase from E. faecalis (MDD EF ). The MDD EF crystal structure in complex with ATP (MDD EF -ATP) revealed that the phosphate-binding loop (amino acids 97-105) is not involved in ATP binding and that the phosphate tail of ATP in this structure is in an outward-facing position pointing away from the active site. This suggested that binding of MDD EF to MVAPP is necessary to guide ATP into a catalytically favorable position. Enzymology experiments show that the MDD EF performs a sequential ordered bi-substrate reaction with MVAPP as the first substrate, consistent with the isothermal titration calorimetry (ITC) experiments. On the basis of ITC results, we propose that this initial prerequisite binding of MVAPP enhances ATP binding. In summary, our findings reveal a substrate-induced substrate-binding event that occurs during the MDD EF -catalyzed reaction. The disengagement of the phosphate-binding loop concomitant with the alternative ATP-binding configuration may provide the structural basis for antimicrobial design against these pathogenic enterococci.


    Organizational Affiliation

    From the Department of Biological Sciences and cstauffa@purdue.edu.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907 and.,From the Department of Biological Sciences and.,the Biophysical Analysis Laboratory, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47906.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mevalonate diphosphate decarboxylase
A
334Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: mvaD
Find proteins for Q837E0 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q837E0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.953α = 90.00
b = 97.684β = 90.00
c = 46.307γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2018-01-10
    Type: Database references