1KNK

Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli involved in Mevalonate-Independent Isoprenoid Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway.

Richard, S.B.Ferrer, J.L.Bowman, M.E.Lillo, A.M.Tetzlaff, C.N.Cane, D.E.Noel, J.P.

(2002) J.Biol.Chem. 277: 8667-8672

  • DOI: 10.1074/jbc.C100739200
  • Primary Citation of Related Structures:  1KNJ

  • PubMed Abstract: 
  • The enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to MECDP, a highly unusual cyclodiphosphate-containing intermediate on the mevalona ...

    The enzyme 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to MECDP, a highly unusual cyclodiphosphate-containing intermediate on the mevalonate-independent pathway to isopentenyl diphosphate and dimethylallyl diphosphate. We now report two x-ray crystal structures of MECDP synthase refined to 2.8-A resolution. The first structure contains a bound Mn(2+) cation, and the second structure contains CMP, MECDP, and Mn(2+). The protein adopts a homotrimeric quaternary structure built around a central hydrophobic cavity and three externally facing active sites. Each of these active sites is located between two adjacent monomers. A tetrahedrally arranged transition metal binding site, potentially occupied by Mn(2+), sits at the base of the active site cleft. A phosphate oxygen of MECDP and the side chains of Asp(8), His(10), and His(42) occupy the metal ion coordination sphere. These structures reveal for the first time the structural determinants underlying substrate, product, and Mn(2+) recognition and the likely catalytic mechanism accompanying the biosynthesis of the cyclodiphosphate-containing isoprenoid precursor, MECDP.


    Related Citations: 
    • Structure of 4-diphosphocytidyl-2-C-methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis
      Richard, S.B.,Bowman, M.E.,Kwiatkowski, W.,Kang, I.,Chow, C.,Lillo, A.M.,Cane, D.E.,Noel, J.P.
      (2001) Nat.Struct.Mol.Biol. 8: 641


    Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A
159Escherichia coli (strain K12)Gene Names: ispF (mecS, ygbB)
EC: 4.6.1.12
Find proteins for P62617 (Escherichia coli (strain K12))
Go to UniProtKB:  P62617
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.232 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 145.630α = 90.00
b = 145.630β = 90.00
c = 145.630γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model