Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.76 kDa 
• Atom Count: 4041 
• Residue Count: 507 
• Unique protein chains: 1

4BQS

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

• DOI: 10.2210/pdb4BQS/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-02 Released: 2013-08-07 
• Deposition Author(s): Otero, J.M., Garcia-Doval, C., Llamas-Saiz, A.L., Blanco, B., Prado, V., Lence, E., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.235 
• R-Value Work: 0.172 
• R-Value Observed: 0.176 

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

• PubMed: 23889343 
• DOI: 10.1021/ja405853p
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SHIKIMATE KINASE	A, B, C	176	Mycobacterium tuberculosis	Mutation(s): 0  EC: 2.7.1.71
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WPY3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B, C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
K2Q	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
K2Q	Ki:  62000   nM  Binding MOAD
K2Q	Ki:  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 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.653	α = 90
b = 60.959	β = 95.44
c = 89.976	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-02 
• Released Date: 2013-08-07 
Deposition Author(s): Otero, J.M., Garcia-Doval, C., Llamas-Saiz, A.L., Blanco, B., Prado, V., Lence, E., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History 

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