3MRS

Crystal structure of shikimate kinase mutant (R57A) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism

Cheng, W.C.Chen, Y.F.Wang, H.J.Hsu, K.C.Lin, S.C.Chen, T.J.Yang, J.M.Wang, W.C.

(2012) Plos One 7: e33481-e33481

  • DOI: 10.1371/journal.pone.0033481
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is pr ...

    Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is present in bacteria, fungi, and plants but absent in mammals and therefore represents an attractive target pathway for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here we investigated the detailed structure-activity relationship of SK from Helicobacter pylori (HpSK). Site-directed mutagenesis and isothermal titration calorimetry studies revealed critical conserved residues (D33, F48, R57, R116, and R132) that interact with shikimate and are therefore involved in catalysis. Crystal structures of HpSK·SO(4), R57A, and HpSK•shikimate-3-phosphate • ADP show a characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132, occupied by shikimate. The structure of the inhibitor complex, E114A • 162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form. These results reveal considerable insight into the active-site chemistry of SKs and a selective inhibitor-induced-fit mechanism.


    Organizational Affiliation

    Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shikimate kinase
A
168Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 1 
Gene Names: aroK
EC: 2.7.1.71
Find proteins for P56073 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56073
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.899α = 90.00
b = 88.899β = 90.00
c = 39.874γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-30
    Type: Database references