4BQS

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with ADP and a shikimic acid derivative.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover.

Blanco, B., Prado, V., Lence, E., Otero, J.M., Garcia-Doval, C., van Raaij, M.J., Llamas-Saiz, A.L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C.

(2013) J. Am. Chem. Soc. 135: 12366-12376

  • DOI: 10.1021/ja405853p

  • PubMed Abstract: 

    • Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and produc ...

    Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and product binding and the enzyme movements that are essential for catalytic turnover of the Mycobacterium tuberculosis shikimate kinase enzyme (Mt-SK) have been investigated by structural and computational studies. Based on these studies several substrate analogs were designed and assayed. The crystal structure of Mt-SK in complex with ADP and one of the most potent inhibitors has been solved at 2.15 Å. These studies reveal that the fixation of the diaxial conformation of the C4 and C5 hydroxyl groups recognized by the enzyme or the replacement of the C3 hydroxyl group in the natural substrate by an amino group is a promising strategy for inhibition because it causes a dramatic reduction of the flexibility of the LID and shikimic acid binding domains. Molecular dynamics simulation studies showed that the product is expelled from the active site by three arginines (Arg117, Arg136, and Arg58). This finding represents a previously unknown key role of these conserved residues. These studies highlight the key role of the shikimic acid binding domain in the catalysis and provide guidance for future inhibitor designs.

    Organizational Affiliation: 

    Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SHIKIMATE KINASE
A, B, C
176Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: aroK
EC: 2.7.1.71
Find proteins for P9WPY2 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WPY2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
K2Q
Query on K2Q
Download SDF File 
Download CCD File 
A, B, C
(1R,6R,10S)-6,10-dihydroxy-2-oxabicyclo[4.3.1]deca-4(Z),7-diene-8-carboxylic acid
C10 H12 O5
RGHXALVTPJSFBL-KHQFGBGNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K2QKi: 62000 nM BINDINGMOAD
K2QKi: 62000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.653α = 90.00
b = 60.959β = 95.44
c = 89.976γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Database references, Structure summary
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation