1UEK

Crystal structure of 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an Enzyme in the Non-mevalonate Pathway of Isoprenoid Synthesis.

Wada, T.Kuzuyama, T.Satoh, S.Kuramitsu, S.Yokoyama, S.Unzai, S.Tame, J.R.Park, S.Y.

(2003) J Biol Chem 278: 30022-30027

  • DOI: 10.1074/jbc.M304339200
  • Primary Citation of Related Structures:  
    1UEK

  • PubMed Abstract: 
  • The crystal structure of the enzyme 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-ME) kinase from the thermophilic bacterium Thermus thermophilus HB8 has been determined at 1.7-A resolution. This enzyme catalyzes phosphorylation of the 2-hydroxyl group of CDP-ME, the fourth step of the non-mevalonate pathway, which is essential for isoprenoid biosynthesis in several pathogenic microorganisms ...

    The crystal structure of the enzyme 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-ME) kinase from the thermophilic bacterium Thermus thermophilus HB8 has been determined at 1.7-A resolution. This enzyme catalyzes phosphorylation of the 2-hydroxyl group of CDP-ME, the fourth step of the non-mevalonate pathway, which is essential for isoprenoid biosynthesis in several pathogenic microorganisms. Since this pathway is absent in humans, it is an important target for the development of novel antimicrobial compounds. The structure of the enzyme is similar to the structures of mevalonate kinase and homoserine kinase, members of the GHMP superfamily. Lys8 and Asp125 are active site residues in mevalonate kinase that also appear to play a catalytic role in CDP-ME kinase. Both the mevalonate and the non-mevalonate pathways therefore involve closely related kinases with similar mechanisms. Assaying the enzyme showed that CDP-ME kinase will phosphorylate CDP-ME but not 4-(uridine 5'-diphospho)-2-C-methyl-D-erythritol, indicating the substrate pyrimidine moiety is involved in important interactions with the enzyme.


    Organizational Affiliation

    Genomic Sciences Center, RIKEN Yokohama Institute, and Protein Design Laboratory, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinaseA275Thermus thermophilusMutation(s): 0 
Gene Names: ychB
EC: 2.7.1.148
UniProt
Find proteins for P83700 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P83700 
Go to UniProtKB:  P83700
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.603α = 90
b = 66.21β = 90
c = 76.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance