Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.29 kDa 
• Atom Count: 2230 
• Residue Count: 268 
• Unique protein chains: 1

1UEK

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

• DOI: 10.2210/pdb1UEK/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-17 Released: 2003-06-17 
• Deposition Author(s): Wada, T., Kuramitsu, S., Yokoyama, S., Tame, J.R.H., Park, S.Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

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 

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

• PubMed: 12771135 
• DOI: 10.1074/jbc.M304339200
• Structures With Same Primary Citation


• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase	A	275	Thermus thermophilus	Mutation(s): 0  Gene Names: ychB EC: 2.7.1.148
Find proteins for P83700 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P83700

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 = 48.603	α = 90
b = 66.21	β = 90
c = 76.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-17 
• Released Date: 2003-06-17 
Deposition Author(s): Wada, T., Kuramitsu, S., Yokoyama, S., Tame, J.R.H., Park, S.Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• 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