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Triose Phosphate Isomerase Structure & Mechanism: Difference between revisions

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==Triose Phosphate Isomerase (TIM)==
==Triose Phosphate Isomerase (TIM)==
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Triose phosphate isomerase (TIM)<ref>PMID:16511037</ref> (PDB [[1wyi]]) 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 (TIM)<ref>PMID:16511037</ref> (PDB [[1wyi]]) 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.
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The enzyme aids in catalysis by binding tightly to the enediol transition state.  To convert GAP to the enediol intermediate, a proton is abstracted from C2 by a base and the carbonyl oxygen atom is protonated by an acid.   
The enzyme aids in catalysis by binding tightly to the enediol transition state.  To convert GAP to the enediol intermediate, a proton is abstracted from C2 by a base and the carbonyl oxygen atom is protonated by an acid.   
<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>  <scene name='Christian_Krenk_Sandbox/Lysine/1'>The enediol intermediate is negatively charged, but is somewhat stabilized by the positively charged side chain of Lys 12.</scene>  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 at their original states, and catalysis is completed.   
<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>  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 at their original states, and catalysis is completed.   


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{{STRUCTURE_1wyi |  PDB=1wyi  |  SCENE=  }}
{{STRUCTURE_1wyi |  PDB=1wyi  |  SCENE=  }}

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Christian Krenk, David Canner, Diamond B. Reese, Michal Harel, Jane S. Richardson, Alexander Berchansky
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