3KE1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with a fragment-nucleoside fusion D000161829


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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 8: e53851-e53851

  • DOI: 10.1016/j.bmcl.2013.09.101
  • Primary Citation of Related Structures:  
    3Q8H, 3KE1

  • PubMed Abstract: 
  • Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP p ...

    Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseABC183Burkholderia pseudomalleiMutation(s): 0 
Gene Names: ispFmecSBPSL2098
EC: 4.6.1.12
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JRA0 
Go to UniProtKB:  Q3JRA0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
829
Query on 829

Download CCD File 
A, B, C
5'-deoxy-5'-[(pyridin-4-ylcarbonyl)amino]cytidine
C15 H17 N5 O5
XQXWUTWGJVGDNS-XIDUGBJDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
829Kd:  180000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.083α = 90
b = 66.964β = 95.42
c = 59.166γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2013-12-11
    Changes: Database references
  • Version 1.4: 2017-11-01
    Changes: Refinement description