Triose Phosphate Isomerase Structure & Mechanism: Difference between revisions
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[[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg|thumb|left|300px|Ribbon drawing for one chain of the "TIM barrel" fold]] | [[Image:TriosePhosphateIsomerase_Ribbon_pastel_photo_small.jpg|thumb|left|300px|Ribbon drawing for one chain of the "TIM barrel" fold]] | ||
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===General Information=== | ===General Information=== | ||
Triose phosphate isomerase (TIM)<ref>PMID:16511037</ref><ref>PMID:8061610</ref> (PDB [[1wyi]] and [[1hti]]) is a crucial enzyme in the glycolytic pathway. <scene name='Christian_Krenk_Sandbox/Nc_rainbow/1'>TIM</scene> reversibly converts the aldose Glyceraldehyde-3-phosphate (GAP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate. Triose phosphate isomerase is not directly regulated, but the enzyme two steps before it in the glycolytic pathway, phosphofructokinase, is a heavily regulated, irreversible enzyme. | Triose phosphate isomerase (TIM)<ref>PMID:16511037</ref><ref>PMID:8061610</ref> (PDB [[1wyi]] and [[1hti]]) is a crucial enzyme in the glycolytic pathway. <scene name='Christian_Krenk_Sandbox/Nc_rainbow/1'>TIM</scene> reversibly converts the aldose Glyceraldehyde-3-phosphate (GAP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate. Triose phosphate isomerase is not directly regulated, but the enzyme two steps before it in the glycolytic pathway, phosphofructokinase, is a heavily regulated, irreversible enzyme. | ||
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<scene name='Christian_Krenk_Sandbox/Active_site/1'> Glu 165 acts as the base and grabs the C2 proton on glyceraldehyde-3-phosphate, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen.</scene> The enediol intermediate is negatively charged, but is somewhat <scene name='Christian_Krenk_Sandbox/Lysine/1'>stabilized by the positively charged side chain of Lys 12.</scene> <ref name= "lodi">PMID:8130193</ref> Mutation of Lys 12 to Arg increases Km by a factor of 22 and decreases Vmax by a factor of 180.<ref name="lodi" /> To convert the enediol intermediate to DHAP, C1 is protonated by Glu 165, with His 95 removing a proton from C2’s OH group. As a result, the catalytic groups are back to their original states, and catalysis is complete. With GAP as a substrate, Km for the reaction is .34 mM and Vmax is 7200 units/mg protein at 25 degrees C and pH 7.5.<ref name= "dab" /> | <scene name='Christian_Krenk_Sandbox/Active_site/1'> Glu 165 acts as the base and grabs the C2 proton on glyceraldehyde-3-phosphate, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen.</scene> The enediol intermediate is negatively charged, but is somewhat <scene name='Christian_Krenk_Sandbox/Lysine/1'>stabilized by the positively charged side chain of Lys 12.</scene> <ref name= "lodi">PMID:8130193</ref> Mutation of Lys 12 to Arg increases Km by a factor of 22 and decreases Vmax by a factor of 180.<ref name="lodi" /> To convert the enediol intermediate to DHAP, C1 is protonated by Glu 165, with His 95 removing a proton from C2’s OH group. As a result, the catalytic groups are back to their original states, and catalysis is complete. With GAP as a substrate, Km for the reaction is .34 mM and Vmax is 7200 units/mg protein at 25 degrees C and pH 7.5.<ref name= "dab" /> | ||
[[Image:ckrenkmechanism.jpg|left|thumb| | [[Image:ckrenkmechanism.jpg|left|thumb|400px| '''Mechanism of Triose phosphate isomerase'''. Created by Christian Krenk using Spartan 08.]] | ||
An interesting part of the enzyme is the <scene name='Christian_Krenk_Sandbox/Flexible_loop/1'>flexible loop</scene> that stabilizes the enediol-like transition state. The flexible loop (residues 167-176)<ref>PMID:2204418</ref> closes over the active site like a hinged lid when substrate is bound, thus preventing phosphate from leaving. A four-residue segment of the loop H-bonds with the phosphate group of the substrate.<ref name="book" /> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref name="book" /> | An interesting part of the enzyme is the <scene name='Christian_Krenk_Sandbox/Flexible_loop/1'>flexible loop</scene> that stabilizes the enediol-like transition state. The flexible loop (residues 167-176)<ref>PMID:2204418</ref> closes over the active site like a hinged lid when substrate is bound, thus preventing phosphate from leaving. A four-residue segment of the loop H-bonds with the phosphate group of the substrate.<ref name="book" /> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref name="book" /> | ||