PDBsum entry 2uzh

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
153 a.a. *
CDP ×3
EDO ×2
GOL ×3
PEG ×2
_ZN ×3
Waters ×272
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Mycobacterium smegmatis 2c-methyl-d-erythritol-2,4- cyclodiphosphate synthase (ispf)
Structure: 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase. Chain: a, b, c. Engineered: yes. Other_details: each contains a zn cation, which is required for activity, and cdp, a fragment of substrate.
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Strain: mc(2)155. Atcc: 700084. Expressed in: escherichia coli. Expression_system_taxid: 469008. From novagen)
2.20Å     R-factor:   0.165     R-free:   0.206
Authors: L.Buetow,A.C.Brown,T.Parish,W.N.Hunter
Key ref: L.Buetow et al. (2007). The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery. BMC Struct Biol, 7, 68. PubMed id: 17956607
27-Apr-07     Release date:   06-Nov-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
A0R559  (A0R559_MYCS2) -  2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
163 a.a.
153 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl- D-erythritol 2,4-cyclodiphosphate + CMP
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
2-C-methyl- D-erythritol 2,4-cyclodiphosphate
Bound ligand (Het Group name = IPE)
matches with 87.00% similarity
Bound ligand (Het Group name = CDP)
matches with 84.00% similarity
      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   3 terms 
  Biochemical function     nucleotide binding     4 terms  


BMC Struct Biol 7:68 (2007)
PubMed id: 17956607  
The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery.
L.Buetow, A.C.Brown, T.Parish, W.N.Hunter.
BACKGROUND: The prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. The 1-deoxy-D-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including Mycobacterium tuberculosis, and is absent from humans. To underpin future drug development it is important to assess which enzymes in this biosynthetic pathway are essential in the actual pathogens and to characterize them. RESULTS: The fifth enzyme of this pathway, encoded by ispF, is 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF). A two-step recombination strategy was used to construct ispF deletion mutants in M. tuberculosis but only wild-type double crossover strains were isolated. The chromosomal copy could be deleted when a second functional copy was provided on an integrating plasmid, demonstrating that ispF is an essential gene under the conditions tested thereby confirming its potential as a drug target. We attempted structure determination of the M. tuberculosis enzyme (MtIspF), but failed to obtain crystals. We instead analyzed the orthologue M. smegmatis IspF (MsIspF), sharing 73% amino acid sequence identity, at 2.2 A resolution. The high level of sequence conservation is particularly pronounced in and around the active site. MsIspF is a trimer with a hydrophobic cavity at its center that contains density consistent with diphosphate-containing isoprenoids. The active site, created by two subunits, comprises a rigid CDP-Zn2+ binding pocket with a flexible loop to position the 2C-methyl-D-erythritol moiety of substrate. Sequence-structure comparisons indicate that the active site and interactions with ligands are highly conserved. CONCLUSION: Our study genetically validates MtIspF as a therapeutic target and provides a model system for structure-based ligand design.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20172995 A.C.Brown, M.Eberl, D.C.Crick, H.Jomaa, and T.Parish (2010).
The nonmevalonate pathway of isoprenoid biosynthesis in Mycobacterium tuberculosis is essential and transcriptionally regulated by Dxs.
  J Bacteriol, 192, 2424-2433.  
20371514 D.García-Moreno, J.Abellón-Ruiz, F.García-Heras, F.J.Murillo, S.Padmanabhan, and M.Elías-Arnanz (2010).
CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD.
  Nucleic Acids Res, 38, 4586-4598.  
  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
18793870 H.Eoh, P.J.Brennan, and D.C.Crick (2009).
The Mycobacterium tuberculosis MEP (2C-methyl-d-erythritol 4-phosphate) pathway as a new drug target.
  Tuberculosis (Edinb), 89, 1.  
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.  
18923920 J.Chen, Y.Xiao, P.Di, X.Yu, W.Chen, and L.Zhang (2009).
Molecular cloning and characterization of a 2C-methyl-D: -erythritol 2,4-cyclodiphosphate synthase gene from Cephalotaxus harringtonia.
  Mol Biol Rep, 36, 1749-1756.  
19320487 N.L.Ramsden, L.Buetow, A.Dawson, L.A.Kemp, V.Ulaganathan, R.Brenk, G.Klebe, and W.N.Hunter (2009).
A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.
  J Med Chem, 52, 2531-2542.
PDB codes: 3elc 3eor 3ern 3esj 3fba
19099550 K.Raman, Y.Kalidas, and N.Chandra (2008).
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.
  BMC Syst Biol, 2, 109.  
18422643 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, and W.N.Hunter (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.
PDB codes: 2v2z 2v34 2v8p
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.