Proteopedia - User contributions [en]

Triose Phosphate Isomerase Structure & Mechanism

2010-03-30T15:29:16Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

===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.

===Structural Characteristics===
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.<ref name= "dab">PMID:752201</ref>

===Mechanism===

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.<ref name= "book">Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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|650px| '''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" />

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

===References===

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-30T15:14:22Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

===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.

===Structural Characteristics===
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.<ref>PMID:752201</ref>

===Mechanism===

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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>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>PMID:8130193</ref> 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>PMID:752201</ref>

[[Image:ckrenkmechanism.jpg|left|thumb|650px| '''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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

===References===

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-30T15:13:00Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

===Structural Characteristics of TIM===
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.<ref>PMID:752201</ref>

===Mechanism of TIM===

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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>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>PMID:8130193</ref> 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>PMID:752201</ref>

[[Image:ckrenkmechanism.jpg|left|thumb|650px| '''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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

===References===

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-23T13:05:54Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.<ref>PMID:752201</ref>

==Mechanism of TIM==

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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>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>PMID:8130193</ref> 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>PMID:752201</ref>

[[Image:ckrenkmechanism.jpg|left|thumb|650px| '''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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

File:Ckrenkmechanism.jpg

2010-03-23T12:56:35Z

Christian Krenk: Triose phosphate isomerase mechanism

== Summary ==
Triose phosphate isomerase mechanism
== Licensing ==
{{PD-self}}

Triose Phosphate Isomerase Structure & Mechanism

2010-03-22T20:14:39Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer. The molecular weight of the enzyme is estimated at 57,400 Da.<ref>PMID:752201</ref>

==Mechanism of TIM==

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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>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>PMID:8130193</ref> 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>PMID:752201</ref>

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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-22T20:07:11Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer.

==Mechanism of TIM==

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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>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>PMID:8130193</ref> 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.

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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T21:02:46Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer.

==Mechanism of TIM==

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.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>
<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 to their original states, and catalysis is complete.

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>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref> Without the loop, the enediol intermediate would eliminate phosphate, with the end products being inorganic phosphate and toxic methylglyoxal.<ref>Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 495. Print.</ref>

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:54:55Z

Christian Krenk:

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:27:34Z

Christian Krenk:

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:21:34Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer.

==Mechanism of TIM==

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> 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.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:18:51Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. The tertiary structure is a <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>alpha-beta barrel.</scene>
The quaternary structure is a homodimer.

==Mechanism of TIM==

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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:16:47Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>The tertiary structure is an alpha-beta barrel.
The quaternary structure is a homodimer.

==Mechanism of TIM==

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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:16:04Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
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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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/2'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
The quaternary structure is a homodimer

==Mechanism of TIM==

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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T20:08:01Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
The quaternary structure is a homodimer

==Mechanism of TIM==

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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T19:52:25Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer, making it fall in the SCOP category of alpha and beta proteins. <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
The quaternary structure is a homodimer

==Mechanism of TIM==

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 GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen.</scene> TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T19:48:38Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==
The secondary structure consists of 14 alpha helices and 8 beta sheets per monomer. <scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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 GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen.</scene> TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T19:45:43Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure:
<scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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'>TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen.</scene> TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T19:17:45Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure:
<scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

{{STRUCTURE_1hti | PDB=1hti | SCENE= }}

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T19:03:49Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure:
<scene name='Christian_Krenk_Sandbox/Alpha_beta_barrel/1'>The tertiary structure is an alpha-beta barrel.</scene>Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T18:52:57Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure: Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

==References==

<references/>

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T18:51:30Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure: Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T13:58:39Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Triose phosphate isomerase (TIM) 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 (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure: Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T13:35:59Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Triose phosphate isomerase (TIM) is a crucial enzyme in the glycolytic pathway. TIM reversibly converts the aldose Glyceraldehyde-3-phosphate (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Structural Characteristics of TIM==

Secondary Structure: Alpha helices and Beta sheets
Tertiary Structure: Alpha/Beta barrel
Quaternary Structure: Homodimer

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

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

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T13:16:14Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Triose phosphate isomerase (TIM) is a crucial enzyme in the glycolytic pathway. TIM reversibly converts the aldose Glyceraldehyde-3-phosphate (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

==Mechanism of TIM==

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. TIM’s Glu 165 acts as the base and grabs GAP’s C2 proton, while His 95 is H-bonded to the carbonyl oxygen and acts as the acid by protonating carbonyl oxygen. The enediol intermediate is negatively charged, but is somewhat stabilized by Lys 12’s positively charged side chain. 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.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T13:13:27Z

Christian Krenk:

==Triose Phosphate Isomerase (TIM)==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
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Triose phosphate isomerase (TIM) is a crucial enzyme in the glycolytic pathway. TIM reversibly converts the aldose Glyceraldehyde-3-phosphate (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}

Triose Phosphate Isomerase Structure & Mechanism

2010-03-01T13:12:37Z

Christian Krenk: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Triose phosphate isomerase (TIM) is a crucial enzyme in the glycolytic pathway. TIM reversibly converts the aldose Glyceraldehyde-3-phosphate (GASP) to the ketose Dihydroxyacetone phosphate (DHAP). The interconversion proceeds by an enediol intermediate.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}