1U43

IspF with 4-diphosphocytidyl-2c-methyl-D-erythritol 2-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase Involved in Mevalonate Independent Biosynthesis of Isoprenoids

Steinbacher, S.Kaiser, J.Wungsintaweekul, J.Hecht, S.Eisenreich, W.Gerhardt, S.Bacher, A.Rohdich, F.

(2002) J Mol Biol 316: 79-88

  • DOI: https://doi.org/10.1006/jmbi.2001.5341
  • Primary Citation of Related Structures:  
    1JY8, 1U3L, 1U3P, 1U40, 1U43

  • PubMed Abstract: 

    Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The non-mevalonate pathway is present in many bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum and in the plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised as promising drug targets. We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction. The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2-phosphate group on the beta-phosphate.


  • Organizational Affiliation

    Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, Martinsried, D-82152, Germany. steinbac@biochem.mpg.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase159Escherichia coliMutation(s): 0 
Gene Names: ispFmecS
EC: 4.6.1.12
UniProt
Find proteins for P62617 (Escherichia coli (strain K12))
Explore P62617 
Go to UniProtKB:  P62617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62617
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SUD
Query on SUD

Download Ideal Coordinates CCD File 
B [auth A]4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL 2-PHOSPHATE
C14 H26 N3 O17 P3
HTJXTKBIUVFUAR-XHIBXCGHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.01α = 90
b = 145.01β = 90
c = 145.01γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations