Sandbox Reserved 763: Difference between revisions
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=Shikimate Kinase= | =Shikimate Kinase= | ||
<Structure load=' | <Structure load='2dfn' size='500' frame='true' align='right' caption='Crystal structure of [[2dfn]] from Protein Data Bank showing shikimate kinase from Mycobacterium tuberculosis complexed with ADP and shikimate.' scene='DefaultScene' /> | ||
[[Image: | [[Image:Binding.PNG|300px|left|thumb| Image showing ADP and shikimate (SKM) bound to SK as a ternary complex [[2dfn]]. Secondary structural elements are also highlighted.]] | ||
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==Structure== | ==Structure== | ||
The crystal structure of [[ | The crystal structure of [[2dfn]] from the Protein Data Bank <ref name="PDB">Protein Data Bank http://www.rcsb.org/pdb/explore.do?structureId=2IYQ</ref> showing shikimate kinase from ''Mycobacterium tuberculosis'' complexed with ADP and shikimate is shown to the right as the <scene name='56/564039/Defaultscene3/1'>default scene</scene>. | ||
===3D Structures in Different Organisms=== | ===3D Structures in Different Organisms=== | ||
Crystal structure have been reported for SK alone, as a binary complex, and as a ternary complex. | Crystal structure have been reported for SK alone, as a binary complex, and as a ternary complex. | ||
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The CORE domain spans from residues 9-17 (phosphate binding loop), 148-155 (AB-loop), and 101-110 (segment which includes alpha6 from 104-110). The SB domain is comprised of residues 32-93 and consists of a sub-domain from residues 32-61 which relates to the NMP-binding domain in NMP kinases. Finally, the LID domain consists of residues 112-124. A global motion leads to LID flapping over the active site upon binding the first substrate (whether shikimate or nucleotide). This causes a change from the open to closed conformation. <ref name="miscinfo">Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium tuberculosis. Journal of Molecular Biology http://www.sciencedirect.com.prox.lib.ncsu.edu/science/article/pii/S0022283606011685#</ref> | The CORE domain spans from residues 9-17 (phosphate binding loop), 148-155 (AB-loop), and 101-110 (segment which includes alpha6 from 104-110). The SB domain is comprised of residues 32-93 and consists of a sub-domain from residues 32-61 which relates to the NMP-binding domain in NMP kinases. Finally, the LID domain consists of residues 112-124. A global motion leads to LID flapping over the active site upon binding the first substrate (whether shikimate or nucleotide). This causes a change from the open to closed conformation. <ref name="miscinfo">Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium tuberculosis. Journal of Molecular Biology http://www.sciencedirect.com.prox.lib.ncsu.edu/science/article/pii/S0022283606011685#</ref> | ||
Understanding the active residues involved in ligand binding is essential to design inhibitors. The P-loop of SK is often targeted by inhibitors as the ATP-binding site catalyzes the reaction (the transfer of a phosphate group). SK binds shikimate at R57, R116, and R132. The hydroxyl groups present on shikimate form contact with M10, D33, G79-81, E114, V44, F48, and R116. The most critical residues for SK catalysis include D33, F48, R57, R116, and R132. It is believed that R57, R132, and F48 form a favorable environment to interact with shikimate, thus triggering a series of conformational changes. Catalyzing the phosphorylation of the 3-hydroxyl group of shikimate is initiated as R116 contacts shikimate during a conformational change.<ref name="compinhibitor"> Structures of Helicobacter pylori Shikimate Kinase Reveal a Selective Inhibitor-Induced-Fit Mechanism. PLoS One. | Understanding the active residues involved in ligand binding is essential to design inhibitors. The P-loop of SK is often targeted by inhibitors as the ATP-binding site catalyzes the reaction (the transfer of a phosphate group). SK binds shikimate at R57, R116, and R132. Shikimate binding occurs with helices α2, α3, and α4 (N-terminal region).<ref name="3dstructure" /> The hydroxyl groups present on shikimate form contact with M10, D33, G79-81, E114, V44, F48, and R116. The most critical residues for SK catalysis include D33, F48, R57, R116, and R132. It is believed that R57, R132, and F48 form a favorable environment to interact with shikimate, thus triggering a series of conformational changes. Catalyzing the phosphorylation of the 3-hydroxyl group of shikimate is initiated as R116 contacts shikimate during a conformational change.<ref name="compinhibitor"> Structures of Helicobacter pylori Shikimate Kinase Reveal a Selective Inhibitor-Induced-Fit Mechanism. PLoS One. | ||
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306394/#!po=19.5652</ref> | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306394/#!po=19.5652</ref> | ||
===Ligands=== | ===Ligands=== | ||
The liganded state of SK includes binary | The liganded state of SK includes binary and ternary complexes. | ||
Examples of ligands include: | |||
<scene name='56/564039/Skmligand/1'>SKM</scene> | |||
<scene name='56/564039/Skm3po4ligand/1'>shikimate 3-phosphate</scene> | |||
<scene name='56/564039/ | <scene name='56/564039/Adpligand/1'>ADP</scene> | ||
<scene name='56/564039/Mgadpligand/1'>MgADP</scene> | <scene name='56/564039/Mgadpligand/1'>MgADP</scene> | ||
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<scene name='56/564039/Atpligand/1'>ATP</scene> | <scene name='56/564039/Atpligand/1'>ATP</scene> | ||
<scene name='56/564039/ | <scene name='56/564039/Clligand/2'>Chloride ion</scene> | ||
<scene name='56/564039/Sulfate/1'>Sulfate</scene> | |||
Magnesium ions bind in the active site and hold influence over the position of shikimate hydroxy groups. This ion has a role in the transfer of the γ-phosphate of ATP to the 3-hydroxy group on shikimate. Chloride ions increase enzyme affinity for ADP and ATP and help to bind the nucleotide substrate in correct orientation.<ref name="mgcl"> Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis Structural Biology and Crystallization Communications | |||
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2330112/</ref> Sulfate is replaced with MgATP in the ternary complex of SK to allow for the reaction to occur.<ref name="sulfate"> Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium tuberculosis. Journal of Molecular Biology. http://www.sciencedirect.com/science/article/pii/S0022283606011685 </ref> SO4 interacts with Arg117 and distorts the nucleotide binding site<ref name="miscinfo" /> | |||
</ref> | |||
===Protein Fold=== | ===Protein Fold=== | ||
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==Implications or Possible Application== | ==Implications or Possible Application== | ||
Enzymes present in the shikimate pathway are important in microorganism survival yet absent in mammals. This means the enzymes of the SKM pathway are good candidates for antimicrobial agents, herbicides, inhibitors, and anti-parasitic drug target. | Enzymes present in the shikimate pathway are important in microorganism survival yet absent in mammals. This means the enzymes of the SKM pathway are good candidates for antimicrobial agents, herbicides, inhibitors, and anti-parasitic drug target. | ||
<ref name="miscinfo" /><ref name="inhibitors" /> | <ref name="miscinfo" /><ref name="inhibitors"> Identification of new potential Mycobacterium tuberculosis shikimate kinase inhibitors through molecular docking simulations. Journal of Molecular Modeling http://link.springer.com.prox.lib.ncsu.edu/article/10.1007%2Fs00894-011-1113-5 | ||
</ref> | |||
Studies of potential inhibitors of SK have been conducted. This is important in the identification of potential drugs against tuberculosis (TB), which is caused by the pathogen ''Mycobacterium tuberculosis.'' TB is a curable infectious disease found mainly in developing countries. Though TB is curable, 100 million people are infected annually with approximately three million resulting deaths. TB resurges as a health problem due to multi-drug resistant, extensively drug resistant, and totally-drug resistant strains of ''Mt''.<ref name="inhibitors" />Disrupting the gene encoding MtSK, ''aroK'', suggests that the shikimate pathway holds great promise for antimicrobial drug discovery.<ref name="compinhibitor" /> | Studies of potential inhibitors of SK have been conducted. This is important in the identification of potential drugs against tuberculosis (TB), which is caused by the pathogen ''Mycobacterium tuberculosis.'' TB is a curable infectious disease found mainly in developing countries. Though TB is curable, 100 million people are infected annually with approximately three million resulting deaths. TB resurges as a health problem due to multi-drug resistant, extensively drug resistant, and totally-drug resistant strains of ''Mt''.<ref name="inhibitors" />Disrupting the gene encoding MtSK, ''aroK'', suggests that the shikimate pathway holds great promise for antimicrobial drug discovery.<ref name="compinhibitor" /> | ||
