1H3M

Structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Tetragonal Crystal Form of Escherichia Coli 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase

Kemp, L.E.Bond, C.S.Hunter, W.N.

(2003) Acta Crystallogr.,Sect.D 59: 607


  • PubMed Abstract: 
  • 2-C-Methyl-D-erythritol 4-phosphate cytidylyltransferase is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. The structure of a tetragonal crystal form has been solved by molecular replacement and refined to 2.4 A ...

    2-C-Methyl-D-erythritol 4-phosphate cytidylyltransferase is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. The structure of a tetragonal crystal form has been solved by molecular replacement and refined to 2.4 A resolution. Structure and sequence comparisons suggest that the enzyme is a suitable target for a structure-based approach to the development of novel broad-spectrum antibiotics. However, the absence of ligands in the enzyme active site together with the moderate resolution of the structure indicates that this tetragonal crystal form is inferior to that of a previously reported highly ordered monoclinic form [Richard et al. (2001), Nature Struct. Biol. 8, 641-647].


    Related Citations: 
    • Structure of Cdp-Me Synthetase in Mevalonate-Independent Isoprenoid Biosynthesis
      Richard, S.B.,Bowman, M.E.,Kwiatkowski, W.,Chow, C.,Lillo, A.M.,Cane, D.E.,Noel, J.P.
      (2001) Nat.Struct.Mol.Biol. 8: 641


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
A, B
235Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ispD (ygbP)
EC: 2.7.7.60
Find proteins for Q46893 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46893
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
N2P
Query on N2P

Download SDF File 
Download CCD File 
A
PENTANE-1,5-DIAMINE
C5 H14 N2
VHRGRCVQAFMJIZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.237 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.604α = 90.00
b = 73.604β = 90.00
c = 175.562γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance