Citrate Synthase: Difference between revisions

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'''Mechanism:''' <scene name='Citrate_Synthase/5ctsactivesitedimer/2'>Three side chains in each of the two active sites</scene> of the dimer contribute directly to the chemistry of catalysis. Focusing on a single active site in the closed conformation, one can easily observe that <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>these three side chains and the two substrates are together</scene> in an arrangement favorable for reaction. (By contrast, <scene name='Citrate_Synthase/Activesite1ctsto2cts/12'>the active site residues are significantly farther apart</scene> in the open conformation; the difference in the distance is ~5Å along the axis that changes the most during the conformation shift.) {{Link Toggle AnimationOnPause}}

The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>. In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>.<br>

The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>. In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>. Citrate synthase is among one of the few enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors.<br>

*In step one, <scene name='Citrate_Synthase/5ctsasp375/9'>Asp 375 acts as a base removing a proton from the methyl group of acetyl-CoA</scene>, resulting in acetyl-CoA forming its enol; His 274 (magenta) stabilizes the acetyl-CoA enol by forming a hydrogen bond with the enol's oxygen. (See the reaction scheme below for a more thorough accounting of the chemistry.)

*In step two (condensation), the <scene name='Citrate_Synthase/5ctscondensation/3'>enol of acetyl-CoA then nucleophilically attacks</scene> oxaloacetate’s carbonyl carbon, and His 320 (cyan) acts as an acid donating a proton to oxaloacetate’s carbonyl group in a concerted step, forming <scene name='Citrate_Synthase/6ctsactivesiteresidues/4'>citryl-CoA</scene> as acetyl-CoA and oxaloacetate become covalently linked; citryl-CoA remains bound to the enzyme at this step in the actual reaction although that linkage is not represented in the 3D structure.

Citrate Synthase: Difference between revisions

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 <table align = 'left' cellpadding='0'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#9999ff'><StructureSection load='Image:5ctsBIOL.pdb.gz' size='380' side='right' scene='Citrate_Synthase/5ctsactivesite/2' caption='Citrate synthase catalysis in the closed conformation'>
 '''Mechanism:''' <scene name='Citrate_Synthase/5ctsactivesitedimer/2'>Three side chains in each of the two active sites</scene> of the dimer contribute directly to the chemistry of catalysis. Focusing on a single active site in the closed conformation, one can easily observe that <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>these three side chains and the two substrates are together</scene> in an arrangement favorable for reaction. (By contrast, <scene name='Citrate_Synthase/Activesite1ctsto2cts/12'>the active site residues are significantly farther apart</scene> in the open conformation; the difference in the distance is ~5&Aring; along the axis that changes the most during the conformation shift.) {{Link Toggle AnimationOnPause}}
-The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>.  In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>.<br>
+The reaction mechanism for citrate synthase was proposed by Remington and colleagues<ref name="1cts">PMID:7120407</ref><ref>PMID: 2337600</ref> and is illustrated here in three dimensions using structures resembling key states of the reaction<ref>[[5cts]] as the state preceding condensation with oxaloacetate and a non-reactive version of acetyl-CoA bound, [[6cts]] as the state containing the bound intermediate, and [[3cts]] as the complex with the products. Positions of hydrogens on the ligands were calculated and added back to structures in the reaction scheme for instructional purposes and are not present in the experimentally-determined structures; additionally, arrows are drawn with atoms of the analog of acetyl-CoA to approximate the position of the reactive groups only as the reactive groups are not actually part of the analog or the molecules would have reacted; please, see the reaction scheme on this page for a more thorough accounting of the chemistry.</ref>.  In this mechanism, three ionizable side chains in the active site of citrate synthase participate in acid-base catalysis: <scene name='Citrate_Synthase/5ctsactivesiteresidues/10'>His 274, His 320, and Asp 375</scene>. Citrate synthase is among one of the few enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors.<br>
 *In step one, <scene name='Citrate_Synthase/5ctsasp375/9'>Asp 375 acts as a base removing a proton from the methyl group of acetyl-CoA</scene>, resulting in acetyl-CoA forming its enol; His 274 (magenta) stabilizes the acetyl-CoA enol by forming a hydrogen bond with the enol's oxygen. (See the reaction scheme below for a more thorough accounting of the chemistry.)
 *In step two (condensation), the <scene name='Citrate_Synthase/5ctscondensation/3'>enol of acetyl-CoA then nucleophilically attacks</scene> oxaloacetate’s carbonyl carbon, and His 320 (cyan) acts as an acid donating a proton to oxaloacetate’s carbonyl group in a concerted step, forming <scene name='Citrate_Synthase/6ctsactivesiteresidues/4'>citryl-CoA</scene> as acetyl-CoA and oxaloacetate become covalently linked; citryl-CoA remains bound to the enzyme at this step in the actual reaction although that linkage is not represented in the 3D structure.