1H48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The Identification of Isoprenoids that Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase by Complementary Biophysical Methods

Kemp, L.E.Alphey, M.S.Bond, C.S.Ferguson, M.Hecht, S.Bacher, A.Eisenreich, W.Rohdich, F.Hunter, W.N.

(2005) Acta Crystallogr D Biol Crystallogr 61: 45

  • DOI: https://doi.org/10.1107/S0907444904025971
  • Primary Citation of Related Structures:  
    1H47, 1H48

  • PubMed Abstract: 

    The discovery of a distinct metabolic pathway, the non-mevalonate or 1-deoxy-D-xylulose-5-phosphate (DOXP) pathway for isoprenoid precursor biosynthesis, in eubacteria and apicomplexan parasites has revealed a new set of potential drug targets. The emphasis of research on this pathway has been on delineating the intermediates and the biochemical and structural characterization of component enzymes. Two new monoclinic crystal forms of recombinant Escherichia coli 2C-methyl-D-erythritol-2,4-cyclodiphosphate (MECP) synthase cocrystallized with (i) CMP and (ii) CMP and MECP show well defined electron density at the subunit interface suggestive of an isoprenoid-like ligand. 31P NMR analysis of the recombinant protein sample indicates the presence of bound diphosphate species and electrospray mass spectrometry identifies a mixture of isopentenyl diphosphate (and/or dimethylallyl diphosphate), geranyl diphosphate and farnesyl diphosphate in an approximate ratio of 1:4:2. The most prevalent species, geranyl diphosphate, was successfully modelled into the electron density, revealing the important protein-ligand interactions that stabilize binding of the isoprenoid. The observation that MECP synthase binds three metabolites that are produced by enzymes two, three and four stages downstream in isoprenoid biosynthesis suggests that feedback regulation of the non-mevalonate pathway is possible.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
A, B, C, D, E
A, B, C, D, E, F
161Escherichia coli BL21Mutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P
Query on C5P

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
N [auth C]
U [auth D]
V [auth E]
I [auth A],
K [auth B],
N [auth C],
U [auth D],
V [auth E],
Z [auth F]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
GPP
Query on GPP

Download Ideal Coordinates CCD File 
Q [auth C],
Y [auth E]
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
CDI
Query on CDI

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AA [auth F]
G [auth A]
L [auth B]
O [auth C]
R [auth D]
AA [auth F],
G [auth A],
L [auth B],
O [auth C],
R [auth D],
W [auth E]
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
C5 H12 O9 P2
SFRQRNJMIIUYDI-UHNVWZDZSA-N
ZN
Query on ZN

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BA [auth F]
H [auth A]
M [auth B]
P [auth C]
S [auth D]
BA [auth F],
H [auth A],
M [auth B],
P [auth C],
S [auth D],
X [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
J [auth A],
T [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.122α = 90
b = 150.287β = 106.52
c = 57.559γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description