5IWX

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway.

Liu, Z.C.Jin, Y.Liu, W.F.Tao, Y.Wang, G.G.

(2018) Biosci Rep 

  • DOI: 10.1042/BSR20171370
  • Primary Citation of Related Structures:  
    5IWX, 5IWY

  • PubMed Abstract: 
  • 2-C-Methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF) is a key enzyme in the 2-C-Methyl-d-erythritol-4-phosphate (MEP) pathway of isoprenoid biosynthesis. This enzyme catalyzes the 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate (CDPME2 ...

    2-C-Methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF) is a key enzyme in the 2-C-Methyl-d-erythritol-4-phosphate (MEP) pathway of isoprenoid biosynthesis. This enzyme catalyzes the 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate (CDPME2P) to 2-C-methyl-d-erythritol 2,4-cyclodiphosphate (MEcDP) with concomitant release of cytidine 5'-diphospate (CMP). Bacillus subtilis is a potential host cell for the production of isoprenoids, but few studies are performed on the key enzymes of MEP pathway in B. subtilis In this work, the high-resolution crystal structures of IspF in native and complex with CMP from B. subtilis have been determined. Structural comparisons indicate that there is a looser packing of the subunits of IspF in B. subtilis , whereas the solvent accessible surface of its active pockets is smaller than that in Escherichia coli. Meanwhile, the protein-protein associations of 2-C-Methyl-d-erythritol-4-phosphatecytidyltransferase (IspD), CDPME kinase (IspE) and IspF from B. subtilis and E. coli , which catalyze three consecutive steps in the MEP pathway, are analyzed by native gel shift and size exclusion chromatography methods. The data here show that protein complex assembly is not detectable. These results will be useful for isoprenoid biosynthesis by metabolic engineering.


    Organizational Affiliation

    Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseABCDEF158Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ispFyacNBSU00910
EC: 4.6.1.12
Find proteins for Q06756 (Bacillus subtilis (strain 168))
Explore Q06756 
Go to UniProtKB:  Q06756
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.964α = 90
b = 89.295β = 100.85
c = 84.708γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references