Isochorismate pyruvate lyase: Difference between revisions
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==Isochorismate== | ==Isochorismate== | ||
Isochorismate is the end product of the shikimate pathway that is essential for the synthesis of many primary and secondary metabolites. It is synthesized from chorismate by isochorismate synthase enzyme. Chorismate is the common precursor for synthesis of aromatic amino acids, cofactors, phenazines and siderophores. | Isochorismate is the end product of the shikimate pathway that is essential for the synthesis of many primary and secondary metabolites. It is synthesized from chorismate by '''isochorismate synthase''' enzyme. Chorismate is the common precursor for synthesis of aromatic amino acids, cofactors, phenazines and siderophores. | ||
Many enzymes are involved in the pathway and these enzymes are present in microbes and plants and absent in mammals and provide potential targets for antimicrobial drugs and herbicides.Isochorismate pyruvate Lyase (IPL) is one such enzyme. | Many enzymes are involved in the pathway and these enzymes are present in microbes and plants and absent in mammals and provide potential targets for antimicrobial drugs and herbicides.Isochorismate pyruvate Lyase (IPL) is one such enzyme<ref>PMID:16248620</ref>. | ||
==Function== | ==Function== | ||
[[Image:superposition of open and closed.png|300px|right]] | [[Image:superposition of open and closed.png|300px|right]] | ||
It is involved in the catalysis of the transformation of isochorismate to pyruvate and salicylate. This reaction is the committed step in the biosynthesis of salicylate-based siderophores in several pathogenic bacteria. In plants, salicylate produced from isochorismate is important for the plant defense mechanisms known as local and systemic acquired resistance It has also been found to have secondary activity of catalyzing the transformation of chorismate to prephenate (chorismate mutase activity), although this is weak. The physiological role of IPL or PchB uses a pericyclic hydrogen transfer mechanism to produce salicylate from isochorismate as opposed to the notion that general base or acid catalysis would occur. This property resembles chorismate mutase enzyme that catalyze pericyclic reactions. IPL is a structural homolog of chorismate mutase despite very low sequence identity (approx 20%). The similarity is restricted to the active sites which are conserved (Annu. Rev. Biophys. 2008. 37:153–73) and it has been found that chorismate mutase cannot be mutated to acquire IPL activity. IPL has been considered for improvement of its secondary activity computationally using hybrid quantum mechanics/ Molecular mechanics (J. AM. CHEM. SOC. 2008, 130, 2894-2895).Homologous genes are found in other microorganisms. It is also involved in bacterial siderophore synthesis. | It is involved in the catalysis of the transformation of isochorismate to pyruvate and salicylate. This reaction is the committed step in the biosynthesis of salicylate-based siderophores in several pathogenic bacteria. In plants, salicylate produced from isochorismate is important for the plant defense mechanisms known as local and systemic acquired resistance It has also been found to have secondary activity of catalyzing the transformation of chorismate to prephenate (chorismate mutase activity), although this is weak. The physiological role of IPL or PchB uses a pericyclic hydrogen transfer mechanism to produce salicylate from isochorismate as opposed to the notion that general base or acid catalysis would occur. This property resembles chorismate mutase enzyme that catalyze pericyclic reactions. IPL is a structural homolog of chorismate mutase[http://www.ebi.ac.uk/pdbsum/1ecm link title] despite very low sequence identity (approx 20%). The similarity is restricted to the active sites which are conserved (Annu. Rev. Biophys. 2008. 37:153–73) and it has been found that chorismate mutase cannot be mutated to acquire IPL activity. IPL has been considered for improvement of its secondary activity computationally using hybrid quantum mechanics/ Molecular mechanics (J. AM. CHEM. SOC. 2008, 130, 2894-2895).Homologous genes are found in other microorganisms. It is also involved in bacterial siderophore synthesis. | ||
Peter Kast et al, propose for PchB a rare [1,5]-sigmatropic reaction mechanism that invokes electrostatic catalysis in analogy to the [3,3]-pericyclic rearrangement of chorismate in Chorismate mutases (CM). | Peter Kast et al, propose for PchB a rare [1,5]-sigmatropic reaction mechanism that invokes electrostatic catalysis in analogy to the [3,3]-pericyclic rearrangement of chorismate in Chorismate mutases (CM). | ||
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==Chemistry== | ==Chemistry== | ||
The transformation of isochorismate to prephenate is a pericyclic reaction. IPL catalyzes the elimination of the enolpyruvyl side chain from isochorismate to give salicylate and pyruvate. This type of aromatization reaction is generally formulated as a baseinitiated process, but a dissociative mechanism involving initial cleavage of the C-O bond to give an ion pair intermediate is conceivable. A concerted pericyclic pathway, in which the hydrogen atom at C2 is transferred to C9 of the side chain simultaneous with C-O cleavage, which represents a third possibility, has been proposed as well. | The transformation of isochorismate to prephenate is a pericyclic reaction. IPL catalyzes the elimination of the enolpyruvyl side chain from isochorismate to give salicylate and pyruvate. This type of aromatization reaction is generally formulated as a baseinitiated process, but a dissociative mechanism involving initial cleavage of the C-O bond to give an ion pair intermediate is conceivable. A concerted pericyclic pathway [http://en.wikipedia.org/wiki/Pericyclic_reaction link title], in which the hydrogen atom at C2 is transferred to C9 of the side chain simultaneous with C-O cleavage, which represents a third possibility, has been proposed as well. | ||
The reaction is a one step mechanism (J. AM. CHEM. SOC. 2005, 127, 15002-15003). | The reaction is a one step mechanism (J. AM. CHEM. SOC. 2005, 127, 15002-15003). | ||
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The resolution abtained for the Apo structure is 2.35 Angstroms and for the pyruvate bound structure it is 1.95 Angstroms. The residues in the loop that connects the first helix to the second has no residues lighting up in the data, depicting the disorderliness. These residues are present in case of the pyruvate bound structures in which case they are ordered. | The resolution abtained for the Apo structure is 2.35 Angstroms and for the pyruvate bound structure it is 1.95 Angstroms. The residues in the loop that connects the first helix to the second has no residues lighting up in the data, depicting the disorderliness. These residues are present in case of the pyruvate bound structures in which case they are ordered. | ||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='2h9dmorph8.pdb' size='390' frame='true' align='right' scene='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Isochorismate-Pyruvate Lyase: open to closed''' (2h9dmorph8.pdb), resolution XXXÅ (<scene name='scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>initial scene</scene>).</center></td></tr></table> | <table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='2h9dmorph8.pdb' size='390' frame='true' align='right' scene='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Isochorismate-Pyruvate Lyase: open to closed morph''' (2h9dmorph8.pdb), resolution XXXÅ (<scene name='scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>initial scene</scene>).</center></td></tr></table> | ||
'''Isochorismate-Pyruvate Lyase: apoenzyme to open conformation with pyruvate bound'''<br> | |||
made by chains A and B of 2h9c morphed to A and B of 2h9d<br> | |||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9cmorph2h9d/2'>here to initiate the animation showing morph of aopenzyme to pyruvate bound to the open confirmation</scene>.<br> | |||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9cmorph2h9dplusside/1'>here</scene> to see sidechains in the morph too.<br> | |||
'''Isochorismate-Pyruvate Lyase: open conformation with pyruvate bound morphing to closed conformation with pyruvate bound'''<br> | |||
made by chains A and B of 2h9d morphed to chains C and D | |||
Click <scene name='User:Wayne_Decatur/Sandboxmangai/2h9d_morph/2'>here to initiate the animation showing morph of open conformation with pyruvate bound morphing to closed conformation with pyruvate bound</scene>.<br> | |||
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==Significance== | ==Significance== | ||
This enzyme unlike others does not catalyze forming covalent enzyme-substrate intermediate or acid-base catalysis. Claisens rearrangement takes place, instead. The substrate is stabilized in an energitically unfavorable pseudoaxial conformation forcing the vanderwaals contact, producing steric strain on the substrate and provides electrostatic stabilization of the transition state. Lys 42 and Gln 90 are positioned to stabilize the developing negative charge of the polar transition product in the chorismate mutase reaction and the pyruvate byproduct in the IPL reaction. therefore the ordering of the active site loop shows induced fit of the enzyme upon substrate binding locks Lys 42 into place for catalysis. | This enzyme unlike others does not catalyze forming covalent enzyme-substrate intermediate or acid-base catalysis. Claisens rearrangement takes place, instead. The substrate is stabilized in an energitically unfavorable pseudoaxial conformation forcing the vanderwaals contact, producing steric strain on the substrate and provides electrostatic stabilization of the transition state. Lys 42 and Gln 90 are positioned to stabilize the developing negative charge of the polar transition product in the chorismate mutase reaction and the pyruvate byproduct in the IPL reaction. therefore the ordering of the active site loop shows induced fit of the enzyme upon substrate binding locks Lys 42 into place for catalysis. | ||
==3D structures of isochorismate pyruvate lyase== | |||
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | |||
[[3log]] – MtIPL/isochorismate synthase - ''Mycobacterium tuberculosis''<br /> | |||
[[3rv6]], [[3rv7]], [[3rv8]], [[3rv9]], [[3st6]], [[3veh]] - MtIPL/isochorismate synthase + inhibitor<br /> | |||
[[2h9c]] – PaIPL residues 1-99 – ''Pseudomonas aeruginosa''<br /> | |||
[[3hgw]] – PaIPL (mutant)<br /> | |||
[[2h9d]] - PaIPL + pyruvate<br /> | |||
[[3rem]] – PaIPL + pyruvate + salicylate<br /> | |||
[[3hgx]], [[3ret]] – PaIPL (mutant) + pyruvate + salicylate<br /> | |||
== References == | |||
<references/> | |||
==Additional Resources== | |||
For additional information, see: [[Amino Acid Synthesis & Metabolism]] | |||
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[[Category:Topic Page]] | |||