Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.228 

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Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.

Kishida, H.Wada, T.Unzai, S.Kuzuyama, T.Takagi, M.Terada, T.Shirouzu, M.Yokoyama, S.Tame, J.R.Park, S.Y.

(2003) Acta Crystallogr D Biol Crystallogr 59: 23-31

  • DOI: https://doi.org/10.1107/s0907444902017705
  • Primary Citation of Related Structures:  
    1IV1, 1IV2, 1IV3, 1IV4

  • PubMed Abstract: 

    Precursors for isoprenoid synthesis are essential in all organisms. These compounds are synthesized by one of two known routes: the well characterized mevalonate pathway or a recently discovered non-mevalonate route which is used in many bacteria and human pathogens. Since the second pathway is both vital and unlike any found in humans, enzymes catalysing reactions along this synthetic route are possible drug targets. The structure of one such enzyme from the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue. Enzyme co-crystallized with substrate shows only one product, cytosine monophosphate (CMP), in the active site. At the high resolution of the refinement (1.6 A) the positions and coordination of the magnesium ions in the active site are clearly seen.

  • Organizational Affiliation

    Protein Design Laboratory, Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase152Thermus thermophilusMutation(s): 0 
Find proteins for Q8RQP5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQP5 
Go to UniProtKB:  Q8RQP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RQP5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.828α = 90
b = 105.828β = 90
c = 148.674γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references