3JVH

Crystal structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with FOL fragment 8395


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.

Begley, D.W.Hartley, R.C.Davies, D.R.Edwards, T.E.Leonard, J.T.Abendroth, J.Burris, C.A.Bhandari, J.Myler, P.J.Staker, B.L.Stewart, L.J.

(2011) J Struct Funct Genomics 12: 63-76

  • DOI: 10.1007/s10969-011-9102-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening ...

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.
      (2013) PLoS One 8: e53851
    • Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.
      Zhang, Z., Jakkaraju, S., Blain, J., Gogol, K., Zhao, L., Hartley, R.C., Karlsson, C.A., Staker, B.L., Edwards, T.E., Stewart, L.J., Myler, P.J., Clare, M., Begley, D.W., Horn, J.R., Hagen, T.J.
      (2013) Bioorg Med Chem Lett --: --

    Organizational Affiliation

    Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. dbegley@embios.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
183Burkholderia pseudomalleiMutation(s): 0 
Gene Names: ispFmecSBPSL2098
EC: 4.6.1.12
Find proteins for Q63T71 (Burkholderia pseudomallei (strain K96243))
Go to UniProtKB:  Q63T71
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HHV
Query on HHV

Download CCD File 
A, B, C
5-[(pyridin-3-ylmethyl)amino]-1H-pyrazole-4-carboxamide
C10 H11 N5 O
LBLVYSJDBWSBHZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.12α = 90
b = 67.65β = 96.32
c = 60γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Database references, Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2013-12-11
    Changes: Database references