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protein ligands metals links
Transferase PDB id
1we2
Jmol
Contents
Protein chain
165 a.a. *
Ligands
ADP
DHK
Metals
_MG
_CL ×2
Waters ×144
* Residue conservation analysis
PDB id:
1we2
Name: Transferase
Title: Crystal structure of shikimate kinase from mycobacterium tuberculosis in complex with mgadp and shikimic acid
Structure: Shikimate kinase. Chain: a. Synonym: sk. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: arok. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.207     R-free:   0.287
Authors: J.H.Pereira,J.S.De Oliveira,F.Canduri,M.V.Dias,M.S.Palma, L.A.Basso,D.S.Santos,W.F.De Azevedo Jr.
Key ref:
J.H.Pereira et al. (2004). Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid. Acta Crystallogr D Biol Crystallogr, 60, 2310-2319. PubMed id: 15583379 DOI: 10.1107/S090744490402517X
Date:
22-May-04     Release date:   17-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A4Z2  (AROK_MYCTU) -  Shikimate kinase
Seq:
Struc: 		176 a.a.
165 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.71  - Shikimate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Shikimate and Chorismate Biosynthesis
      Reaction: ATP + shikimate = ADP + shikimate 3-phosphate
ATP
 +
shikimate
Bound ligand (Het Group name = DHK)
corresponds exactly 		=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ shikimate 3-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     growth   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S090744490402517X Acta Crystallogr D Biol Crystallogr 60:2310-2319 (2004)
PubMed id: 15583379  
 
 
Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
J.H.Pereira, J.S.de Oliveira, F.Canduri, M.V.Dias, M.S.Palma, L.A.Basso, D.S.Santos, W.F.de Azevedo.
 
  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.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 F[obs] - F[calc] electron density contoured at 3.0 [234][sigma] showing the binding of shikimate. The figure was prepared with XtalView (McRee, 1999[235] [McRee, D. E. (1999). J. Struct. Biol. 125, 156-165.]-[236][bluearr.gif] ). 		Figure 6.
Figure 6 The molecular structure of shikimate shows the carboxyl group and three hydroxyl groups. C atoms are numbered in blue and O atoms in red.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 2310-2319) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19043750 G.B.Barcellos, R.A.Caceres, and W.F.de Azevedo (2009).
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP.
  J Mol Model, 15, 147-155.  
18343960 R.A.Caceres, L.F.Macedo Timmers, A.L.Vivan, C.Z.Schneider, L.A.Basso, W.F.De Azevedo, and D.S.Santos (2008).
Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.
  J Mol Model, 14, 427-434.  
  17183161 M.V.Dias, L.M.Faím, I.B.Vasconcelos, J.S.de Oliveira, L.A.Basso, D.S.Santos, and W.F.de Azevedo (2007).
Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1-6.
PDB codes: 2dfn 2dft
15759144 N.J.Silveira, H.B.Uchôa, J.H.Pereira, F.Canduri, L.A.Basso, M.S.Palma, D.S.Santos, and W.F.de Azevedo (2005).
Molecular models of protein targets from Mycobacterium tuberculosis.
  J Mol Model, 11, 160-166.  
16291688 W.C.Cheng, Y.N.Chang, and W.C.Wang (2005).
Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase.
  J Bacteriol, 187, 8156-8163.
PDB codes: 1zuh 1zui
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.