3QT5

Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis.

Barta, M.L.Skaff, D.A.McWhorter, W.J.Herdendorf, T.J.Miziorko, H.M.Geisbrecht, B.V.

(2011) J.Biol.Chem. 286: 23900-23910

  • DOI: 10.1074/jbc.M111.242016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The polyisoprenoid compound undecaprenyl phosphate is required for biosynthesis of cell wall peptidoglycans in gram-positive bacteria, including pathogenic Enterococcus, Streptococcus, and Staphylococcus spp. In these organisms, the mevalonate pathwa ...

    The polyisoprenoid compound undecaprenyl phosphate is required for biosynthesis of cell wall peptidoglycans in gram-positive bacteria, including pathogenic Enterococcus, Streptococcus, and Staphylococcus spp. In these organisms, the mevalonate pathway is used to produce the precursor isoprenoid, isopentenyl 5-diphosphate. Mevalonate diphosphate decarboxylase (MDD) catalyzes formation of isopentenyl 5-diphosphate in an ATP-dependent irreversible reaction and is therefore an attractive target for inhibitor development that could lead to new antimicrobial agents. To facilitate exploration of this possibility, we report the crystal structure of Staphylococcus epidermidis MDD (1.85 Å resolution) and, to the best of our knowledge, the first structures of liganded MDD. These structures include MDD bound to the mevalonate 5-diphosphate analogs diphosphoglycolyl proline (2.05 Å resolution) and 6-fluoromevalonate diphosphate (FMVAPP; 2.2 Å resolution). Comparison of these structures provides a physical basis for the significant differences in K(i) values observed for these inhibitors. Inspection of enzyme/inhibitor structures identified the side chain of invariant Ser(192) as making potential contributions to catalysis. Significantly, Ser → Ala substitution of this side chain decreases k(cat) by ∼10(3)-fold, even though binding interactions between FMVAPP and this mutant are similar to those observed with wild type MDD, as judged by the 2.1 Å cocrystal structure of S192A with FMVAPP. Comparison of microbial MDD structures with those of mammalian counterparts reveals potential targets at the active site periphery that may be exploited to selectively target the microbial enzymes. These studies provide a structural basis for previous observations regarding the MDD mechanism and inform future work toward rational inhibitor design.


    Organizational Affiliation

    Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mevalonate diphosphate decarboxylase
A, B
332Staphylococcus epidermidisMutation(s): 0 
Gene Names: mvaD
EC: 4.1.1.33
Find proteins for Q9FD73 (Staphylococcus epidermidis)
Go to UniProtKB:  Q9FD73
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.983α = 90.00
b = 101.987β = 90.00
c = 155.771γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-23
    Type: Database references