Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.31 kDa 
• Atom Count: 1412 
• Residue Count: 165 
• Unique protein chains: 1

1WE2

Crystal structure of shikimate kinase from mycobacterium tuberculosis in complex with MGADP and shikimic acid

• DOI: 10.2210/pdb1WE2/pdb

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


• Deposited: 2004-05-22 Released: 2005-05-17 
• Deposition Author(s): Pereira, J.H., de Oliveira, J.S., Canduri, F., Dias, M.V., Palma, M.S., Basso, L.A., Santos, D.S., de Azevedo Jr., W.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.287 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.

Pereira, J.H., de Oliveira, J.S., Canduri, F., Dias, M.V., Palma, M.S., Basso, L.A., Santos, D.S., de Azevedo, W.F.

(2004) Acta Crystallogr D Biol Crystallogr 60: 2310-2319

• PubMed: 15583379 
• DOI: 10.1107/S090744490402517X
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Tuberculosis made a resurgence in the mid-1980s and now kills approximately 3 million people a year. The re-emergence of tuberculosis as a public health threat, the high susceptibility of HIV-infected persons and the proliferation of multi-drug-resistant strains have created a need to develop new drugs. Shikimate kinase and other enzymes in the shikimate pathway are attractive targets for development of non-toxic antimicrobial agents, herbicides and anti-parasitic drugs, because the pathway is essential in these species whereas it is absent from mammals. The crystal structure of shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (shikimate) has been determined at 2.3 A resolution, clearly revealing the amino-acid residues involved in shikimate binding. This is the first three-dimensional structure of shikimate kinase complexed with shikimate. In MtSK, the Glu61 residue that is strictly conserved in shikimate kinases forms a hydrogen bond and salt bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for shikimate binding. The carboxyl group of shikimate interacts with Arg58, Gly81 and Arg136 and the hydroxyl groups interact with Asp34 and Gly80. The crystal structure of MtSK-MgADP-shikimate will provide crucial information for the elucidation of the mechanism of the shikimate kinase-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.

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Organizational Affiliation: 

Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Shikimate kinase	A	176	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: aroK EC: 2.7.1.71
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WPY3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DHK	A	3-DEHYDROSHIKIMATE C7 H10 O5 YVYKOQWMJZXRRM-UYFOZJQFSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DHK	Kd:  44000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.287 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.91	α = 90
b = 62.91	β = 90
c = 90.92	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-22 
• Released Date: 2005-05-17 
Deposition Author(s): Pereira, J.H., de Oliveira, J.S., Canduri, F., Dias, M.V., Palma, M.S., Basso, L.A., Santos, D.S., de Azevedo Jr., W.F.

Revision History 

• Version 1.0: 2005-05-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance