2WW4

a triclinic crystal form of E. coli 4-diphosphocytidyl-2C-methyl-D- erythritol kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Triclinic Crystal Form of Escherichia Coli 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase and Reassessment of the Quaternary Structure.

Kalinowska-Tluscik, J.Miallau, L.Gabrielsen, M.Leonard, G.A.Mcsweeney, S.M.Hunter, W.N.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 237

  • DOI: https://doi.org/10.1107/S1744309109054591
  • Primary Citation of Related Structures:  
    2WW4

  • PubMed Abstract: 

    4-Diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-D-xylulose 5-phosphate or mevalonate-independent biosynthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-D-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-D-erythritol. A triclinic crystal structure of the Escherichia coli IspE-ADP complex with two molecules in the asymmetric unit was determined at 2 A resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the ;triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization.


  • Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College 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
4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE
A, B
283Escherichia coliMutation(s): 0 
EC: 2.7.1.148
UniProt
Find proteins for P62615 (Escherichia coli (strain K12))
Explore P62615 
Go to UniProtKB:  P62615
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62615
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.051α = 88.77
b = 50.124β = 69.65
c = 66.035γ = 65.14
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references, Derived calculations, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description