PDBsum entry 2v34

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
269 a.a. *
CTN ×2
SO4 ×8
_CL ×2
Waters ×493
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Ispe in complex with cytidine and ligand
Structure: 4-diphosphocytidyl-2c-methyl-d-erythritol kinase. Chain: a, b. Synonym: cmk, 4-cytidine-5'-diphospho-2-c-methyl-d- erythritol kinase. Engineered: yes
Source: Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.30Å     R-factor:   0.199     R-free:   0.245
Authors: T.Sgraja,M.S.Alphey,W.N.Hunter
Key ref: T.Sgraja et al. (2008). Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery. FEBS J, 275, 2779-2794. PubMed id: 18422643
11-Jun-07     Release date:   26-Jun-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O67060  (ISPE_AQUAE) -  4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
268 a.a.
269 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Bound ligand (Het Group name = CTN)
matches with 51.00% similarity
+ 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
      Cofactor: Mn(2+) or Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     isoprenoid biosynthetic process   4 terms 
  Biochemical function     nucleotide binding     5 terms  


FEBS J 275:2779-2794 (2008)
PubMed id: 18422643  
Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery.
T.Sgraja, M.S.Alphey, S.Ghilagaber, R.Marquez, M.N.Robertson, J.L.Hemmings, S.Lauw, F.Rohdich, A.Bacher, W.Eisenreich, V.Illarionova, W.N.Hunter.
4-Diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE) catalyses the ATP-dependent conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol (CDPME) to 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate with the release of ADP. This reaction occurs in the non-mevalonate pathway of isoprenoid precursor biosynthesis and because it is essential in important microbial pathogens and absent from mammals it represents a potential target for anti-infective drugs. We set out to characterize the biochemical properties, determinants of molecular recognition and reactivity of IspE and report the cloning and purification of recombinant Aquifex aeolicus IspE (AaIspE), kinetic data, metal ion, temperature and pH dependence, crystallization and structure determination of the enzyme in complex with CDP, CDPME and ADP. In addition, 4-fluoro-3,5-dihydroxy-4-methylpent-1-enylphosphonic acid (compound 1) was designed to mimic a fragment of the substrate, a synthetic route to 1 was elucidated and the complex structure determined. Surprisingly, this ligand occupies the binding site for the ATP alpha-phosphate not the binding site for the methyl-D-erythritol moiety of CDPME. Gel filtration and analytical ultracentrifugation indicate that AaIspE is a monomer in solution. The enzyme displays the characteristic alpha/beta galacto-homoserine-mevalonate-phosphomevalonate kinase fold, with the catalytic centre positioned in a deep cleft between the ATP- and CDPME-binding domains. Comparisons indicate a high degree of sequence conservation on the IspE active site across bacterial species, similarities in structure, specificity of substrate recognition and mechanism. The biochemical characterization, attainment of well-ordered and reproducible crystals and the models resulting from the analyses provide reagents and templates to support the structure-based design of broad-spectrum antimicrobial agents.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20208151 J.Kalinowska-Tłuścik, L.Miallau, M.Gabrielsen, G.A.Leonard, S.M.McSweeney, and W.N.Hunter (2010).
A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C-methyl-D-erythritol kinase and reassessment of the quaternary structure.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 237-241.
PDB code: 2ww4
20189102 P.Narayanasamy, H.Eoh, P.J.Brennan, and D.C.Crick (2010).
Synthesis of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate and kinetic studies of Mycobacterium tuberculosis IspF.
  Chem Biol, 17, 117-122.  
20064433 H.Eoh, P.Narayanasamy, A.C.Brown, T.Parish, P.J.Brennan, and D.C.Crick (2009).
Expression and characterization of soluble 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from bacterial pathogens.
  Chem Biol, 16, 1230-1239.  
18633530 A.K.Hirsch, M.S.Alphey, S.Lauw, M.Seet, L.Barandun, W.Eisenreich, F.Rohdich, W.N.Hunter, A.Bacher, and F.Diederich (2008).
Inhibitors of the kinase IspE: structure-activity relationships and co-crystal structure analysis.
  Org Biomol Chem, 6, 2719-2730.
PDB code: 2vf3
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