Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase fromMycobacterium tuberculosis

Abstract

PDB References: shikimate kinase-ADPshikimate complex, 2dfn, r2dfnsf; shikimate kinase-MgADP complex, 2dft, r2dftsf.Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts shikimate to shikimate-3-phosphate. In this work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.

New tuberculosis drug development: targeting the shikimate pathway

“…However, insights into the chemical and kinetic mechanisms of the enzyme have recently been published [83,84] . By contrast, substantially more work has been performed on the fifth and sixth enzymes of the pathway: SK and EPSP [56,57,59,60,69,94] . Two small molecular inhibitors against Helicobacter pylori shikimate kinase have recently been identified through high-throughput screening: 3-methoxy-4-{[2-({2-methoxy-4-[(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy}methyl)benzyl]oxy} benzaldehyde and 5-bromo-2-(5-{[1-(3,4-dichlorophenyl)-3,5-dioxo-4-pyrazolidinylidene]methyl}-2-furyl)benzoic acid.…”

“…For example, although the crystal structure of the E. coli DAHP synthase, the first enzyme of the shikimate pathway, has been known for some time [89] , only recently has the preliminary M. tuberculosis DAHP synthase three-dimensional structure ADP Shikimate Figure 3 . M. tuberculosis shikimate kinase complexed with shikimate and ADP [69] .…”

“…Although few inhibition studies have been performed involving the M. tuberculosis SK (MtSK) enzyme [66] , the elucidation of the crystal structure of MtSK [59,67] allowed for the detailed study of the enzyme and related target-ligand interactions [60,[68][69][70] . Among the specific SK interfaces studied has been the role of the ADP/Mg 2+ complex in creating the correct geometry to complete the phosphoryl transfer essential for the formation of S3P [59,71] .…”

Inhibition of Shikimate Kinase and Type II Dehydroquinase for Antibiotic Discovery: Structure-Based Design and Simulation Studies

“…The SB domain is highly conserved and involves a number of charged residues, specifically Arg136, Arg58, Glu61, Asp34, Arg117 and Lys15, and a lipophilic pocket formed by Phe49, Phe57, Pro118, Gly79, Gly80 and Gly81 (in Mt-SK). Circular dichroism [21], fluorescence [22] and structural [20][21][22][23][24] studies suggested that ATP first binds to the enzyme and induces a large movement of the LID domain over the active site. Shikimic acid (6) subsequently binds to the active site and the LID domain closes over the active site and brings Arg110 and Arg117 into the ATP and SB domains, respectively [20].…”

“…These important features have encouraged diverse research groups to study in detail the substrate binding requirements of this enzyme [20][21][22][23][24][25]. As a result, several crystal structures of SK, mainly from M. tuberculosis, have been reported, either as binary complexes with ATP, ADP or shikimic acid (6) in the active site, or as tertiary complexes with ADP/shikimic acid (6) or ADP/shikimate 3-phosphate (7) [20][21][22][23]. These structures have been an excellent starting point for the structure-based design of inhibitors, which will be discussed below.…”