1W77

2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

Gabrielsen, M.Kaiser, J.Rohdich, F.Eisenreich, W.Laupitz, R.Bacher, A.Bond, C.S.Hunter, W.N.

(2006) FEBS J. 273: 1065

  • DOI: 10.1111/j.1742-4658.2006.05133.x
  • Also Cited By: 2YCM, 2YC5, 2YC3

  • PubMed Abstract: 
  • 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 th ...

    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.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
A
228Arabidopsis thalianaMutation(s): 1 
Gene Names: ISPD (MCT, MECT, MEPCT)
EC: 2.7.7.60
Find proteins for P69834 (Arabidopsis thaliana)
Go to Gene View: ISPD
Go to UniProtKB:  P69834
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5P
Query on C5P

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.232 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 74.496α = 90.00
b = 74.496β = 90.00
c = 223.026γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
BEASTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance