PDBsum entry 1w77

Go to PDB code: 
protein ligands metals links
Transferase PDB id
Protein chain
212 a.a. *
_CU ×4
Waters ×166
* Residue conservation analysis
PDB id:
Name: Transferase
Title: 2c-methyl-d-erythritol 4-phosphate cytidylyltransferase (ispd) from arabidopsis thaliana
Structure: 2c-methyl-d-erythritol 4-phosphate cytidylyltransferase. Chain: a. Fragment: cytidyltransferase domain, residues 76-302. Synonym: 4-diphosphocytidyl-2c-methyl-d-erythritol synthase, putative sugar nucleotide phosphorylase. Engineered: yes. Mutation: yes. Other_details: chloroplast targeting sequence removed,
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.00Å     R-factor:   0.237     R-free:   0.349
Authors: M.Gabrielsen,J.Kaiser,F.Rohdich,W.Eisenreich,A.Bacher, C.S.Bond,W.N.Hunter
Key ref:
M.Gabrielsen et al. (2006). The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphate. FEBS J, 273, 1065-1073. PubMed id: 16478479 DOI: 10.1111/j.1742-4658.2006.05133.x
30-Aug-04     Release date:   21-Feb-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P69834  (ISPD_ARATH) -  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
302 a.a.
212 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Bound ligand (Het Group name = C5P)
matches with 72.00% similarity
+ 2-C-methyl-D-erythritol 4-phosphate
= diphosphate
+ 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
      Cofactor: Manganese or magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     isoprenoid biosynthetic process   1 term 
  Biochemical function     catalytic activity     1 term  


DOI no: 10.1111/j.1742-4658.2006.05133.x FEBS J 273:1065-1073 (2006)
PubMed id: 16478479  
The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphate.
M.Gabrielsen, J.Kaiser, F.Rohdich, W.Eisenreich, R.Laupitz, A.Bacher, C.S.Bond, W.N.Hunter.
The homodimeric 2C-methyl-d-erythritol 4-phosphate cytidylyltransferase contributes to the nonmevalonate pathway of isoprenoid biosynthesis. The crystal structure of the catalytic domain of the recombinant enzyme derived from the plant Arabidopsis thaliana has been solved by molecular replacement and refined to 2.0 A resolution. The structure contains cytidine monophosphate bound in the active site, a ligand that has been acquired from the bacterial expression system, and this observation suggests a mechanism for feedback regulation of enzyme activity. Comparisons with bacterial enzyme structures, in particular the enzyme from Escherichia coli, indicate that whilst individual subunits overlay well, the arrangement of subunits in each functional dimer is different. That distinct quaternary structures are available, in conjunction with the observation that the protein structure contains localized areas of disorder, suggests that conformational flexibility may contribute to the function of this enzyme.
  Selected figure(s)  
Figure 1.
Fig. 1. The reaction catalysed by 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) in the context of the nonmevalonate route to isoprenoid precursors.
Figure 6.
Fig. 6. (A and B) Orthogonal views of the Arabidopsis thaliana IspD (AthIspD) dimer. Subunits are coloured green and cyan, -helices are depicted as cylinders, and -strands as shown as arrows. Cytidine monophosphate (CMP) is shown as spheres with atoms coloured according to type: C, yellow; N, blue; O, red; and P, pink. (C and D) Corresponding views showing an overlay of AthIspD and EcIspD (coloured grey). The overlay in Fig. 3 corresponds to the C atoms of the green AthIspD subunit superimposed with one subunit of EcIspD. Selected elements of secondary structure are labelled on the subunits not used in the least squares superposition. In panel D, the arrow indicates the direction of rotation of an AthIspD subunit with respect to EcIspD.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2006, 273, 1065-1073) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21543842 C.Björkelid, T.Bergfors, L.M.Henriksson, A.L.Stern, T.Unge, S.L.Mowbray, and T.A.Jones (2011).
Structural and functional studies of mycobacterial IspD enzymes.
  Acta Crystallogr D Biol Crystallogr, 67, 403-414.
PDB codes: 2xwl 2xwm 2xwn
17442674 W.N.Hunter (2007).
The non-mevalonate pathway of isoprenoid precursor biosynthesis.
  J Biol Chem, 282, 21573-21577.  
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 codes are shown on the right.