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2015-04-26T22:31:07Z

Stephanie Raynor:

2015-04-26T03:53:54Z

Stephanie Raynor:

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2015-04-26T03:21:01Z

Stephanie Raynor:

==''Mycobacterium tuberculosis'' salicylate synthase (Mbt1)==
<StructureSection load='3LOG' size='450' side='right' caption='Structure of MbtI ([[3LOG]])'>

==Introduction==
<scene name='69/694235/3log/12'>Salicylate synthase</scene> from ''Mycobacterium tuberculosis'' (MtbI) is a highly promiscuous enzyme that has four distinct activities ''in vivo'': [http://en.wikipedia.org/wiki/Isochorismate_synthase isochorismate synthase] (IS), [http://www.proteopedia.org/wiki/index.php/Isochorismate_pyruvate_lyase isochorismate pyruvate lyase] (IPL), [http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=8A8773E9&tabtoshow=Current salicylate synthase] (SS) and [http://en.wikipedia.org/wiki/Chorismate_mutase chorismate mutate] (CM). MtbI belongs to the chorismate-utilising enzyme family, which consists of structural homologues (<scene name='69/694235/Irp9/5'>Ipr9</scene>, <scene name='69/694235/Menf/3'>MenF</scene>, <scene name='69/694235/Entc/3'>EntC</scene>, and <scene name='69/694235/Mbti/3'>MbtI</scene>) that isomerize chromate to isochorismate. These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis. The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation. IS, IPL, and SS activity are also modulated by the pH of the medium. Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8.
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating [http://en.wikipedia.org/wiki/Siderophore siderophore], mycobactin, in ''Mycobacterium tuberculosis'' (Figure 3)<ref name= "5a">PMID:22607697</ref>. This complex secondary metabolite is essential for both virulence and survival of ''M. tuberculosis''. Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action <ref name= "1a"> DOI: 10.1002/cmdc/201000137</ref> <ref name= "2a">PMID:23108268</ref> <ref name= "7a">Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.</ref> <ref name= "5a"/> <ref name= "4a">DOI:10.1021/bi2009739</ref> <ref name= "9a">PMID:14982443</ref>

[[Image:Pathways.png|500 px|center|thumb|Figure 1: This is the pathway of reactions catilized by wild-type MbtI <ref>PMID:22307014</ref>.]]

==Structure==
[[Image:Active_site_cleft.png|300 px|left|thumb|Figure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.]]
The crystal asymmetric unit was found to contain <scene name='69/694235/3log/11'> four MbtI molecules</scene>, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme. There are no significant structural changes between the four monomers excepts from the localized differences in the active site <ref name= "3a">PMID 15342575</ref>. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes <ref name="3a"/>. The core of the protein is formed by <scene name='69/694234/Beta_sheets/1'>21 Beta sheets </scene>folded into a twisted beta-sandwich. The protein's core is then surrounded by <scene name='69/694235/Beta_sheets/4'>10 alpha helices</scene><ref name="3a"/>.

<scene name='69/694235/Alpha_helics/2'>TextToBeDisplayed</scene>

<scene name='69/694235/Beta_strands/2'>TextToBeDisplayed</scene>

== Structural highlights ==
MtI structure has a mobile element (residues 323 to 227) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site. The closed conformation partially obstructs the active site. <ref name= "5a"/>.

Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate. Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone. Positioning of the active site residues of MbtI with the inhibitor AMT is highly similar to the closed form of MbtI <ref name= "5a"/>.

==Molecular Mechanism==
'''Magnesium cation effect'''
[[Image:Screen Shot 2015-04-25 at 11.08.58 PM.png‎ |300 px|left|thumb|'''Table 1:''' pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]] The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity(Table 1) . The coordination shell of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.

'''Isochorismate pyruvate lyase (IPL)'''

Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.

[[Image:IPL2.png|500 px|center|thumb|Figure 3: Isochorismate pyruvate activity <ref>PMID:22307014</ref>.]]

'''Isochorismate synthase (IS)'''

Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group <ref>PMID:14982443</ref>. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.

[[Image:IS2.png|500 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

'''chorismate mutase (CM)'''

A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.

[[Image:CM2.png|450 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

== Disease ==
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] is the causative agent of [http://www.cdc.gov/tb/ Tuberculosis] (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide <ref>Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.</ref>. Although various treatments for TB infection and TB disease exist, the emergence of [http://www.cdc.gov/tb/publications/factsheets/drtb/mdrtb.htm multi-drug] and [http://www.cdc.gov/tb/topic/drtb/xdrtb.htm extensively-drug] resistant strains of ''M. tuberculosis'' has increased the need for anti-tubercular agents with novel modes of action.

[http://en.wikipedia.org/wiki/Iron#Biological_role Iron] is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.''M. tuberculosis'' obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.

Mycobactin is a siderophore synthesized by the proteins encoded by the ''mbt'' and ''mbt2'' gene clusters <ref name="5a"/>. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)

MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of ''M. tuberculosis''<ref>De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.</ref> .

[[Image:Screen Shot 2015-04-10 at 1.27.15 PM.png‎|500 px|center|thumb|Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway<ref name= "2a"/>.]]

==Inhibition Studies==

MbtI Inhibition studies aid in the future design of [http://psychology.wikia.com/wiki/Antitubercular_drugs anti-tubercular agents] and [http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic broad-spectrum antibiotics] with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, <scene name='69/694235/3sr6_inhibitor/3'>isochorismate</scene>, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate <ref name= "1a"/>. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.

Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.

IsochorismateSpecifically, <scene name='69/694235/3rv6_with_vae1/1'>2-hydroxybenzoate-based inhibitors</scene> that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.

<scene name='69/694235/3veh_structure/2'>TextToBeDisplayed</scene>
<scene name='69/694235/3veh_structure_bindingpocket/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure_bindingpocket/1'>TextToBeDisplayed</scene>
</StructureSection>
== References ==
{{reflist}}

==Student contributors==
Stephanie Raynor and Robin Gagnon

==Similar Pages==
[http://proteopedia.org/wiki/index.php/2i6y 2i6y]

==Related pdb files==
[[3LOG]]

Sandbox Reserved 1068

2015-04-26T03:17:59Z

Stephanie Raynor:

==''Mycobacterium tuberculosis'' salicylate synthase (Mbt1)==
<StructureSection load='3LOG' size='450' side='right' caption='Structure of MbtI ([[3LOG]])'>

==Introduction==
<scene name='69/694235/3log/12'>Salicylate synthase</scene> from ''Mycobacterium tuberculosis'' (MtbI) is a highly promiscuous enzyme that has four distinct activities ''in vivo'': [http://en.wikipedia.org/wiki/Isochorismate_synthase isochorismate synthase] (IS), [http://www.proteopedia.org/wiki/index.php/Isochorismate_pyruvate_lyase isochorismate pyruvate lyase] (IPL), [http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=8A8773E9&tabtoshow=Current salicylate synthase] (SS) and [http://en.wikipedia.org/wiki/Chorismate_mutase chorismate mutate] (CM). MtbI belongs to the chorismate-utilising enzyme family, which consists of structural homologues (<scene name='69/694235/Irp9/5'>Ipr9</scene>, <scene name='69/694235/Menf/3'>MenF</scene>, <scene name='69/694235/Entc/3'>EntC</scene>, and <scene name='69/694235/Mbti/3'>MbtI</scene>) that isomerize chromate to isochorismate. These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis. The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation. IS, IPL, and SS activity are also modulated by the pH of the medium. Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8.
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating [http://en.wikipedia.org/wiki/Siderophore siderophore], mycobactin, in ''Mycobacterium tuberculosis'' (Figure 3)<ref name= "5a">PMID:22607697</ref>. This complex secondary metabolite is essential for both virulence and survival of ''M. tuberculosis''. Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action <ref name= "1a"> DOI: 10.1002/cmdc/201000137</ref> <ref name= "2a">PMID:23108268</ref> <ref name= "7a">Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.</ref> <ref name= "5a"/> <ref name= "4a">DOI:10.1021/bi2009739</ref> <ref name= "9a">PMID:14982443</ref>

[[Image:Pathways.png|500 px|center|thumb|Figure 1: This is the pathway of reactions catilized by wild-type MbtI <ref>PMID:22307014</ref>.]]

==Structure==
[[Image:Active_site_cleft.png|300 px|left|thumb|Figure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.]]
The crystal asymmetric unit was found to contain <scene name='69/694235/3log/11'> four MbtI molecules</scene>, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme. There are no significant structural changes between the four monomers excepts from the localized differences in the active site <ref name= "3a">PMID 15342575</ref>. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes <ref name="3a"/>. The core of the protein is formed by <scene name='69/694234/Beta_sheets/1'>21 Beta sheets </scene>folded into a twisted beta-sandwich. The protein's core is then surrounded by <scene name='69/694235/Beta_sheets/4'>10 alpha helices</scene><ref name="3a"/>.

<scene name='69/694235/Alpha_helics/2'>TextToBeDisplayed</scene>

<scene name='69/694235/Beta_strands/2'>TextToBeDisplayed</scene>

== Structural highlights ==
MtI structure has a mobile element (residues 323 to 227) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site. The closed conformation partially obstructs the active site. <ref name= "5a"/>.

Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate. Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone. Positioning of the active site residues of MbtI with the inhibitor AMT is highly similar to the closed form of MbtI <ref name= "5a"/>.

==Molecular Mechanism==
'''Magnesium cation effect'''
[[Image:Screen Shot 2015-04-25 at 11.08.58 PM.png‎ |300 px|left|thumb|Table 1: pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]]
The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity . The coordination shell of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.

'''Isochorismate pyruvate lyase (IPL)'''

Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.

[[Image:IPL2.png|500 px|center|thumb|Figure 3: Isochorismate pyruvate activity <ref>PMID:22307014</ref>.]]

'''Isochorismate synthase (IS)'''

Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group <ref>PMID:14982443</ref>. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.

[[Image:IS2.png|500 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

'''chorismate mutase (CM)'''

A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.

[[Image:CM2.png|450 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

== Disease ==
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] is the causative agent of [http://www.cdc.gov/tb/ Tuberculosis] (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide <ref>Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.</ref>. Although various treatments for TB infection and TB disease exist, the emergence of [http://www.cdc.gov/tb/publications/factsheets/drtb/mdrtb.htm multi-drug] and [http://www.cdc.gov/tb/topic/drtb/xdrtb.htm extensively-drug] resistant strains of ''M. tuberculosis'' has increased the need for anti-tubercular agents with novel modes of action.

[http://en.wikipedia.org/wiki/Iron#Biological_role Iron] is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.''M. tuberculosis'' obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.

Mycobactin is a siderophore synthesized by the proteins encoded by the ''mbt'' and ''mbt2'' gene clusters <ref name="5a"/>. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)

MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of ''M. tuberculosis''<ref>De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.</ref> .

[[Image:Screen Shot 2015-04-10 at 1.27.15 PM.png‎|500 px|center|thumb|Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway<ref name= "2a"/>.]]

==Inhibition Studies==

MbtI Inhibition studies aid in the future design of [http://psychology.wikia.com/wiki/Antitubercular_drugs anti-tubercular agents] and [http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic broad-spectrum antibiotics] with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, <scene name='69/694235/3sr6_inhibitor/3'>isochorismate</scene>, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate <ref name= "1a"/>. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.

Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.

IsochorismateSpecifically, <scene name='69/694235/3rv6_with_vae1/1'>2-hydroxybenzoate-based inhibitors</scene> that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.

<scene name='69/694235/3veh_structure/2'>TextToBeDisplayed</scene>
<scene name='69/694235/3veh_structure_bindingpocket/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure_bindingpocket/1'>TextToBeDisplayed</scene>
</StructureSection>
== References ==
{{reflist}}

==Student contributors==
Stephanie Raynor
Robin Gagnon

==Similar Pages==
[http://proteopedia.org/wiki/index.php/2i6y 2i6y]

==Related pdb files==
[[3LOG]]

Sandbox Reserved 1068

2015-04-26T03:15:47Z

Stephanie Raynor:

==''Mycobacterium tuberculosis'' salicylate synthase (Mbt1)==
<StructureSection load='3LOG' size='450' side='right' caption='Structure of MbtI ([[3LOG]])'>

==Introduction==
<scene name='69/694235/3log/12'>Salicylate synthase</scene> from ''Mycobacterium tuberculosis'' (MtbI) is a highly promiscuous enzyme that has four distinct activities ''in vivo'': [http://en.wikipedia.org/wiki/Isochorismate_synthase isochorismate synthase] (IS), [http://www.proteopedia.org/wiki/index.php/Isochorismate_pyruvate_lyase isochorismate pyruvate lyase] (IPL), [http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=8A8773E9&tabtoshow=Current salicylate synthase] (SS) and [http://en.wikipedia.org/wiki/Chorismate_mutase chorismate mutate] (CM). MtbI belongs to the chorismate-utilising enzyme family, which consists of structural homologues (<scene name='69/694235/Irp9/5'>Ipr9</scene>, <scene name='69/694235/Menf/3'>MenF</scene>, <scene name='69/694235/Entc/3'>EntC</scene>, and <scene name='69/694235/Mbti/3'>MbtI</scene>) that isomerize chromate to isochorismate. These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis. The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation. IS, IPL, and SS activity are also modulated by the pH of the medium. Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8.
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating [http://en.wikipedia.org/wiki/Siderophore siderophore], mycobactin, in ''Mycobacterium tuberculosis'' (Figure 3)<ref name= "5a">PMID:22607697</ref>. This complex secondary metabolite is essential for both virulence and survival of ''M. tuberculosis''. Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action <ref name= "1a"> DOI: 10.1002/cmdc/201000137</ref> <ref name= "2a">PMID:23108268</ref> <ref name= "7a">Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.</ref> <ref name= "5a"/> <ref name= "4a">DOI:10.1021/bi2009739</ref> <ref name= "9a">PMID:14982443</ref>

[[Image:Pathways.png|500 px|center|thumb|Figure 1: This is the pathway of reactions catilized by wild-type MbtI <ref>PMID:22307014</ref>.]]

==Structure==
[[Image:Active_site_cleft.png|300 px|left|thumb|Figure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.]]
The crystal asymmetric unit was found to contain <scene name='69/694235/3log/11'> four MbtI molecules</scene>, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme. There are no significant structural changes between the four monomers excepts from the localized differences in the active site <ref name= "3a">PMID 15342575</ref>. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes <ref name="3a"/>. The core of the protein is formed by <scene name='69/694234/Beta_sheets/1'>21 Beta sheets </scene>folded into a twisted beta-sandwich. The protein's core is then surrounded by <scene name='69/694235/Beta_sheets/4'>10 alpha helices</scene><ref name="3a"/>.

<scene name='69/694235/Alpha_helics/2'>TextToBeDisplayed</scene>

<scene name='69/694235/Beta_strands/2'>TextToBeDisplayed</scene>

== Structural highlights ==
MtI structure has a mobile element (residues 323 to 227) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site. The closed conformation partially obstructs the active site. <ref name= "5a"/>.

Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate. Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone. Positioning of the active site residues of MbtI with the inhibitor AMT is highly similar to the closed form of MbtI <ref name= "5a"/>.

==Molecular Mechanism==
'''Magnesium cation effect'''

The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity . The coordination shell of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.

[[Image:Screen Shot 2015-04-25 at 11.08.58 PM.png‎ |500 px|center|thumb|Table 1: pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]]

'''Isochorismate pyruvate lyase (IPL)'''

Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.

[[Image:IPL2.png|500 px|center|thumb|Figure 3: Isochorismate pyruvate activity <ref>PMID:22307014</ref>.]]

'''Isochorismate synthase (IS)'''

Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group <ref>PMID:14982443</ref>. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.

[[Image:IS2.png|500 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

'''chorismate mutase (CM)'''

A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.

[[Image:CM2.png|450 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

== Disease ==
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] is the causative agent of [http://www.cdc.gov/tb/ Tuberculosis] (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide <ref>Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.</ref>. Although various treatments for TB infection and TB disease exist, the emergence of [http://www.cdc.gov/tb/publications/factsheets/drtb/mdrtb.htm multi-drug] and [http://www.cdc.gov/tb/topic/drtb/xdrtb.htm extensively-drug] resistant strains of ''M. tuberculosis'' has increased the need for anti-tubercular agents with novel modes of action.

[http://en.wikipedia.org/wiki/Iron#Biological_role Iron] is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.''M. tuberculosis'' obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.

Mycobactin is a siderophore synthesized by the proteins encoded by the ''mbt'' and ''mbt2'' gene clusters <ref name="5a"/>. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)

MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of ''M. tuberculosis''<ref>De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.</ref> .

[[Image:Screen Shot 2015-04-10 at 1.27.15 PM.png‎|500 px|center|thumb|Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway<ref name= "2a"/>.]]

==Inhibition Studies==

MbtI Inhibition studies aid in the future design of [http://psychology.wikia.com/wiki/Antitubercular_drugs anti-tubercular agents] and [http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic broad-spectrum antibiotics] with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, <scene name='69/694235/3sr6_inhibitor/3'>isochorismate</scene>, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate <ref name= "1a"/>. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.

Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.

IsochorismateSpecifically, <scene name='69/694235/3rv6_with_vae1/1'>2-hydroxybenzoate-based inhibitors</scene> that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.

<scene name='69/694235/3veh_structure/2'>TextToBeDisplayed</scene>
<scene name='69/694235/3veh_structure_bindingpocket/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure_bindingpocket/1'>TextToBeDisplayed</scene>
</StructureSection>
== References ==
{{reflist}}

==Student contributors==
Stephanie Raynor
Robin Gagnon

==Similar Pages==
[http://proteopedia.org/wiki/index.php/2i6y 2i6y]

==Related pdb files==
[[3LOG]]

Sandbox Reserved 1068

2015-04-26T03:13:50Z

Stephanie Raynor:

==''Mycobacterium tuberculosis'' salicylate synthase (Mbt1)==
<StructureSection load='3LOG' size='450' side='right' caption='Structure of MbtI ([[3LOG]])'>

==Introduction==
<scene name='69/694235/3log/12'>Salicylate synthase</scene> from ''Mycobacterium tuberculosis'' (MtbI) is a highly promiscuous enzyme that has four distinct activities ''in vivo'': [http://en.wikipedia.org/wiki/Isochorismate_synthase isochorismate synthase] (IS), [http://www.proteopedia.org/wiki/index.php/Isochorismate_pyruvate_lyase isochorismate pyruvate lyase] (IPL), [http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=8A8773E9&tabtoshow=Current salicylate synthase] (SS) and [http://en.wikipedia.org/wiki/Chorismate_mutase chorismate mutate] (CM). MtbI belongs to the chorismate-utilising enzyme family, which consists of structural homologues (<scene name='69/694235/Irp9/5'>Ipr9</scene>, <scene name='69/694235/Menf/3'>MenF</scene>, <scene name='69/694235/Entc/3'>EntC</scene>, and <scene name='69/694235/Mbti/3'>MbtI</scene>) that isomerize chromate to isochorismate. These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis. The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation. IS, IPL, and SS activity are also modulated by the pH of the medium. Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8.
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating [http://en.wikipedia.org/wiki/Siderophore siderophore], mycobactin, in ''Mycobacterium tuberculosis'' (Figure 3)<ref name= "5a">PMID:22607697</ref>. This complex secondary metabolite is essential for both virulence and survival of ''M. tuberculosis''. Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action <ref name= "1a"> DOI: 10.1002/cmdc/201000137</ref> <ref name= "2a">PMID:23108268</ref> <ref name= "7a">Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.</ref> <ref name= "5a"/> <ref name= "4a">DOI:10.1021/bi2009739</ref> <ref name= "9a">PMID:14982443</ref>

[[Image:Pathways.png|500 px|center|thumb|Figure 1: This is the pathway of reactions catilized by wild-type MbtI <ref>PMID:22307014</ref>.]]

==Structure==
[[Image:Active_site_cleft.png|300 px|left|thumb|Figure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.]]
The crystal asymmetric unit was found to contain <scene name='69/694235/3log/11'> four MbtI molecules</scene>, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme. There are no significant structural changes between the four monomers excepts from the localized differences in the active site <ref name= "3a">PMID 15342575</ref>. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes <ref name="3a"/>. The core of the protein is formed by <scene name='69/694234/Beta_sheets/1'>21 Beta sheets </scene>folded into a twisted beta-sandwich. The protein's core is then surrounded by <scene name='69/694235/Beta_sheets/4'>10 alpha helices</scene><ref name="3a"/>.

<scene name='69/694235/Alpha_helics/2'>TextToBeDisplayed</scene>

<scene name='69/694235/Beta_strands/2'>TextToBeDisplayed</scene>

== Structural highlights ==
MtI structure has a mobile element (residues 323 to 227) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site. The closed conformation partially obstructs the active site. <ref name= "5a"/>.

Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate. Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone. Positioning of the active site residues of MbtI with the inhibitor AMT is highly similar to the closed form of MbtI <ref name= "5a"/>.

==Molecular Mechanism==
'''Magnesium cation effect'''

The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity . The coordination shell of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.

[[Image:Image:Screen Shot 2015-04-25 at 11.08.58 PM.png‎ |500 px|center|thumb|Table 1: pKa values of active site residues of MbtI with and without Magnesium. Ferrer 2-11.]]

'''Isochorismate pyruvate lyase (IPL)'''

Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.

[[Image:IPL2.png|500 px|center|thumb|Figure 3: Isochorismate pyruvate activity <ref>PMID:22307014</ref>.]]

'''Isochorismate synthase (IS)'''

Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group <ref>PMID:14982443</ref>. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.

[[Image:IS2.png|500 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

'''chorismate mutase (CM)'''

A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.

[[Image:CM2.png|450 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

== Disease ==
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] is the causative agent of [http://www.cdc.gov/tb/ Tuberculosis] (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide <ref>Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.</ref>. Although various treatments for TB infection and TB disease exist, the emergence of [http://www.cdc.gov/tb/publications/factsheets/drtb/mdrtb.htm multi-drug] and [http://www.cdc.gov/tb/topic/drtb/xdrtb.htm extensively-drug] resistant strains of ''M. tuberculosis'' has increased the need for anti-tubercular agents with novel modes of action.

[http://en.wikipedia.org/wiki/Iron#Biological_role Iron] is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.''M. tuberculosis'' obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.

Mycobactin is a siderophore synthesized by the proteins encoded by the ''mbt'' and ''mbt2'' gene clusters <ref name="5a"/>. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)

MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of ''M. tuberculosis''<ref>De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.</ref> .

[[Image:Screen Shot 2015-04-10 at 1.27.15 PM.png‎|500 px|center|thumb|Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway<ref name= "2a"/>.]]

==Inhibition Studies==

MbtI Inhibition studies aid in the future design of [http://psychology.wikia.com/wiki/Antitubercular_drugs anti-tubercular agents] and [http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic broad-spectrum antibiotics] with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, <scene name='69/694235/3sr6_inhibitor/3'>isochorismate</scene>, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate <ref name= "1a"/>. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.

Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.

IsochorismateSpecifically, <scene name='69/694235/3rv6_with_vae1/1'>2-hydroxybenzoate-based inhibitors</scene> that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.

<scene name='69/694235/3veh_structure/2'>TextToBeDisplayed</scene>
<scene name='69/694235/3veh_structure_bindingpocket/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure/1'>TextToBeDisplayed</scene>

<scene name='69/694235/3st6_structure_bindingpocket/1'>TextToBeDisplayed</scene>
</StructureSection>
== References ==
{{reflist}}

==Student contributors==
Stephanie Raynor
Robin Gagnon

==Similar Pages==
[http://proteopedia.org/wiki/index.php/2i6y 2i6y]

==Related pdb files==
[[3LOG]]

2015-04-25T19:58:50Z

Stephanie Raynor:

==''Mycobacterium tuberculosis'' salicylate synthase (Mbt1)==
<StructureSection load='3LOG' size='450' side='right' caption='Structure of MbtI ([[3LOG]])'>

==Introduction==
<scene name='69/694235/3log/7'>Salicylate synthase</scene> from ''Mycobacterium tuberculosis'' (MtbI) is a highly promiscuous enzyme that has four distinct activities ''in vivo'': [http://en.wikipedia.org/wiki/Isochorismate_synthase isochorismate synthase] (IS), [http://www.proteopedia.org/wiki/index.php/Isochorismate_pyruvate_lyase isochorismate pyruvate lyase] (IPL), [http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=8A8773E9&tabtoshow=Current salicylate synthase] (SS) and [http://en.wikipedia.org/wiki/Chorismate_mutase chorismate mutate] (CM). MtbI belongs to the chorismate-utilising enzyme family, which consists of structural homologues (<scene name='69/694235/Irp9/2'>Ipr9</scene>, <scene name='69/694235/Menf/2'>MenF</scene>, <scene name='69/694235/Entc/2'>EntC</scene>, and <scene name='69/694235/Mbti/2'>MbtI</scene>) that isomerize chromate to isochorismate. These enzymes are present in bacteria, fungi, plants and apicomplexan parasites and catalyze the initial reactions of menaquinone, siderophore, and tryptophan biosynthesis. The IS, IPL, and SS activity of MbtI require the presence of a magnesium ion within the active site, while CM activity is only observed in absence of the magnesium cation. IS, IPL, and SS activity are also modulated by the pH of the medium. Isochorismate is the primary product at pH values below 7.5 and salicylate is the primary product formed at pH 8.
The salicylate synthase activity of MbtI catalyzes the first committed step in the synthesis of the iron chelating [http://en.wikipedia.org/wiki/Siderophore siderophore], mycobactin, in ''Mycobacterium tuberculosis'' (Figure 3)<ref name= "5a">PMID:22607697</ref>. This complex secondary metabolite is essential for both virulence and survival of ''M. tuberculosis''. Therefore, inhibitors of salicylate synthase may serve as potential TB therapies with a novel mode of action <ref name= "1a"> DOI: 10.1002/cmdc/201000137</ref> <ref name= "2a">PMID:23108268</ref> <ref name= "7a">Voss, James J., Kerry Rutter, Benjamin G. Schroedor, Hua Su, and YaQi Zhu. "The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages." Proceedings of the National Academy of Sciences 97.3 (2000): 1252-57. Web. 14 Mar. 2015.</ref> <ref name= "5a"/> <ref name= "4a">DOI:10.1021/bi2009739</ref> <ref name= "9a">PMID:14982443</ref>

[[Image:Pathways.png|500 px|center|thumb|Figure 1: This is the pathway of reactions catilized by wild-type MbtI <ref>PMID:22307014</ref>.]]

==Structure==
[[Image:Active_site_cleft.png|300 px|left|thumb|Figure 2: This shows a single sub unit of MbtI, with the active site cleft located at the lower left hand side of the image.]]
The crystal asymmetric unit was found to contain <scene name='69/694235/3log/1'> four MbtI molecules</scene>, however crystal packing and size exclusion chromatography data suggest a monomeric enzyme. There are no significant structural changes between the four monomers excepts from the localized differences in the active site <ref name= "3a">PMID 15342575</ref>. The overall molecular structure consist of a polypeptide of 450 residues that forms one large single domain with a similar fold to other chromate-utilizing enzymes <ref name="3a"/>. The core of the protein is formed by <scene name='69/694234/Beta_sheets/1'>21 Beta sheets </scene>folded into a twisted beta-sandwich. The protein's core is then surrounded by <scene name='69/694235/Beta_sheets/4'>10 alpha helices</scene><ref name="3a"/>.

== Structural highlights ==
MtI structure has a mobile element (residues 323 to 227) that can adopt a <scene name='69/694235/Irp9_closed_state/2'>closed</scene> or <scene name='69/694235/2g5f_with_open_loop/1'>open conformation</scene> depending on whether or not ligands are bound to the active site. The closed conformation partially obstructs the active site. <ref name= "5a"/>.

Inhibition studies have also shown a switch in binding mode at the MbtI active site for inhibitors carrying a substituted enolpyruvyl group compared to the chorismate substrate. Crystal structures and fluorescent-based thermal shift assays show that substituents larger than a methyl group are accommodated in the active site of MbtI through localized flexibility in the peptide backbone. Positioning of the active site residues of MbtI with the inhibitor AMT is highly similar to the closed form of MbtI <ref name= "5a"/>.

==Molecular Mechanism==
'''Magnesium cation effect'''

The presence of the [http://en.wikipedia.org/wiki/Magnesium_in_biology magnesium ion] induces <scene name='69/694235/Mg_coordination/1'>changes in the structure</scene> of the active site and in the substrate, as well as causes significant pKa shifts in some of the key residues involved in the catalytic activity . The coordination shell of the magnesium cation in the active site of MbtI is composed of two water molecules, Glu434, Glu294, and the two oxygen atoms of the C1 carboxylate group of chorismate <ref name= "8a">PMID:22307014</ref>. In the presence of the magnesium ion, the positively charged Lys295 is displaced from the active site and the negatively charged Glu297 is faced toward the active site. Magnesium cation also orients the C1 carboxylate group coplanar to the ring of chorismate, reducing the electron density on the C2 center and favoring nucleophilic attack.

'''Isochorismate pyruvate lyase (IPL)'''

Isochorismate is converted to salicylate and pyruvate through abstraction of the C2 hydrogen followed by protonation of C9 atom and the breakage of the C3-O7 bond. Histidine residue (His334) was proposed to act as a base, abstracting the C2 proton of isochorismate through a second order elimination mechanism. However, recent studies have shown that this residue lies more than 13 A away from C2 atom and no other water molecules appear close enough to the C2 atom to act as a base. IPL reaction has been proposed to proceed through an intramolecular pericyclic mechanisms, involving a concerted hydrogen transfer from C2 to C9 and breakage of the C3-O7 bond.

[[Image:IPL2.png|500 px|center|thumb|Figure 3: Isochorismate pyruvate activity <ref>PMID:22307014</ref>.]]

'''Isochorismate synthase (IS)'''

Currently, isochorismate is believed to be formed from chorismate through a proposed Sn2 mechanism involving nucleophilic attack of an activated water molecule to the C2 center followed by either a concerted or stepwise elimination of the C4 hydroxyl group <ref>PMID:14982443</ref>. Lys205 has been proposed to act as the catalytic base, activating a water molecule in the active site by abstracting one of its protons. However, mutational analysis of Lys205 suggested that the lysine reside is not the sole determinant in the activation of a water molecule for nucleophilic attack of the C2 center. Studies have shown that Lys205 is protonated at neutral pH and therefore can't act as a base to activate the water molecule, agreeing with the mutational analysis data. Instead of Lys205, Glu297 residue has been proposed to act as a base in the activation of the water molecule. The magnesium ion forces the negatively charged Glu297 residue to face toward the active site and the pKa of Glu297 (3.9) suggest an unprotonated state. Furthermore, Glu297 forms a hydrogen bond with a water molecule within the active site as well as with Lys205, which is in turn hydrogen bonded to C1 carboxylate group of chorismate and the oxygen of the nucleophilic water molecule. The glutamic residue (Gly252) could protonate the C4 leaving hydroxyl group. The pKa of Gly252 (7.7) suggest that is it is the only protonated glutamate residue in the active site at pH 7 and thus able to protonate the C4 leaving group. The pKa of Gly252 also accounts for the accumulation of isochorismate at pH values below 7.5.

[[Image:IS2.png|500 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

'''chorismate mutase (CM)'''

A magnesium ion in the active site orients the C1 carboxyl group of chorismate. A lysine residue then serves as a general base for the activation of a water molecule to attack at C2. The catalytic mechanism for conversion of isochorismate to salicylate by MbtI is a sigmatropic, pericyclic mechanism that is pH-dependent. Chromate mutase activity is only observed in the absence of magnesium ion in the active site while salicylate synthase activity is depended on magnesium ion. The active site of MbtI is altered by the removal of the magnesium cofactor causing chromate mutase activity. MbtI has differing binding modes for chromate that leads to different substrate conformations/transition states and resulting in different products.

[[Image:CM2.png|450 px|center|thumb|Figure 3: Isochorismate synthase activity <ref>PMID:22307014</ref>.]]

== Disease ==
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] is the causative agent of [http://www.cdc.gov/tb/ Tuberculosis] (TB), an infectious disease that affects one-third of the worlds population. Two TB-related conditions exist: latent TB infection and active TB disease. Currently, there are four regimens that are approved for the treatment of latent TB infection through the use of the antibiotics isoniazid, rifampin, and rifapentine.TB disease can also be treated through various antibiotic regimens. There are 10 drugs currently approved by the FDA for treating TB disease. The first-line anti-TB agents are the antibiotics isoniazid, rifampin, ethambutol, and pyrazinamide <ref>Tuberculosis (TB). Ed. Sam Posner. Centers for Disease Control and Prevention, n.d. Web. 9 Apr. 2015.</ref>. Although various treatments for TB infection and TB disease exist, the emergence of [http://www.cdc.gov/tb/publications/factsheets/drtb/mdrtb.htm multi-drug] and [http://www.cdc.gov/tb/topic/drtb/xdrtb.htm extensively-drug] resistant strains of ''M. tuberculosis'' has increased the need for anti-tubercular agents with novel modes of action.

[http://en.wikipedia.org/wiki/Iron#Biological_role Iron] is essential for mycobacterial growth and pathogenesis, therefore the pathways for iron acquisition are potential targets for antibacterial therapies.''M. tuberculosis'' obtains iron through two different pathways: chelating iron from the host through the siderophore mycobactin and the degradation of heme released from damaged red blood cells.

Mycobactin is a siderophore synthesized by the proteins encoded by the ''mbt'' and ''mbt2'' gene clusters <ref name="5a"/>. The gene Rv2386c is essential for the in vitro growth of "M. tuberculosis" and codes the enzyme MbtI. (turvey, 2010)

MbtI catalyses the first committed step in the biosynthesis of the siderophore mycobactin and is a potential target for inhibition. The salicylate synthase activity of MbtI produces salicylate and pyruvate from chorismate through an isochorismate intermediate. Inhibition of MbtI activity would decrease the production of salicylate and therefore the synthesis of mycobactin; leading to a decrease in iron acquisition and pathogenesis of ''M. tuberculosis''<ref>De Voss, James J., Kerry Rutter, Benjamin G. Schroeder, Hua Su, and YaQi Zhu. The salicylate-derived mycobacterium siderophore of Mycobacterium tuberculosis are essential for growth in macrophages. "Proceedings of the National Science Academy" 97.3 (2000): 1252-57. Web. 5 Apr. 2015.</ref> .

[[Image:Screen Shot 2015-04-10 at 1.27.15 PM.png‎|500 px|center|thumb|Figure 3: Reaction catalyzed by MbtI in the mycobactin biosynthesis pathway<ref name= "2a"/>.]]

==Inhibition Studies==

MbtI Inhibition studies aid in the future design of [http://psychology.wikia.com/wiki/Antitubercular_drugs anti-tubercular agents] and [http://en.wikipedia.org/wiki/Broad-spectrum_antibiotic broad-spectrum antibiotics] with a novel mode of action. Mimics of the enzyme-bound intermediate of MbtI, <scene name='69/694235/3sr6_inhibitor/1'>isochorismate</scene>, prove to be significantly more potent inhibitors than mimics of the substrate, chorismate <ref name= "1a"/>. The isochorismate mimic based on a 2,3-dihydroxybenzoate scaffold showed low-micromolar inhibition constants against MbtI that were an order of magnitude more potents than the natural substrates. The most potent inhibitors contained hydrophobic enol ether side chains at C3 instead of the enol-pyruvyl side chains seen in chorismate and isochorismate (Turvey 2010). Increased potency of inhibitors with a substituted enolpyruvyl group has been attributed to a change in the binding mode through localized flexibility of the peptide backbone.

Two binding mode at the MbtI active site have been observed based on the structure of the inhibitor.

IsochorismateSpecifically, <scene name='69/694235/3rv6_with_vae1/1'>2-hydroxybenzoate-based inhibitors</scene> that contain extended hydrophobic enol ether side chains at C3 in place of the enol-pyruvate side chain found in chorismate and isochorismate.

</StructureSection>
== References ==
{{reflist}}

==Student contributors==
Stephanie Raynor
Robin Gagnon

==Similar Pages==
[http://proteopedia.org/wiki/index.php/2i6y 2i6y]

==Related pdb files==
[[3LOG]]