3SZU

IspH:HMBPP complex structure of E126Q mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Mutant IspH Proteins Reveal a Rotation of the Substrate's Hydroxymethyl Group during Catalysis.

Span, I.Grawert, T.Bacher, A.Eisenreich, W.Groll, M.

(2012) J.Mol.Biol. 416: 1-9

  • DOI: 10.1016/j.jmb.2011.11.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Isoprenoids derive from two universal precursors, isopentenyl diphosphate and dimethylallyl diphosphate, which in most human pathogens are synthesized in the deoxyxylulose phosphate pathway. The last step of this pathway is the conversion of (E)-1-hy ...

    Isoprenoids derive from two universal precursors, isopentenyl diphosphate and dimethylallyl diphosphate, which in most human pathogens are synthesized in the deoxyxylulose phosphate pathway. The last step of this pathway is the conversion of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate into a mixture of isopentenyl diphosphate and dimethylallyl diphosphate catalyzed by the iron-sulfur protein IspH. The crystal structures reported here of the IspH mutant proteins T167C, E126D and E126Q reveal an alternative substrate conformation compared to the wild-type structure. Thus, the previously observed alkoxide complex decomposes, and the substrate's hydroxymethyl group rotates to interact with Glu126. The carboxyl group of Glu126 then donates a proton to the hydroxyl group to enable water elimination. The structural and functional studies provide further knowledge of the IspH reaction mechanism, which opens up new routes to inhibitor design against malaria and tuberculosis.


    Organizational Affiliation

    Chemistry Department, Center for Integrated Protein Science, Chair of Biochemistry, Technische Universit√§t M√ľnchen, Lichtenbergstrasse 4, 85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
A, B
328Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ispH (lytB, yaaE)
EC: 1.17.7.4
Find proteins for P62623 (Escherichia coli (strain K12))
Go to UniProtKB:  P62623
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
H6P
Query on H6P

Download SDF File 
Download CCD File 
A, B
(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
C5 H12 O8 P2
MDSIZRKJVDMQOQ-GORDUTHDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.190α = 90.00
b = 80.390β = 90.00
c = 112.010γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
XDSdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references
  • Version 1.2: 2012-02-15
    Type: Database references