Proteopedia - User contributions [en]

Fructuronate-tagaturonate epimerase

2022-06-26T21:35:36Z

Daniel Barzilay:

==Structure==

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
The structure comprises 490 amino acids, a metal ion and a phosphate ion. Each protomer consisted of four do mains: core domain (CD), extra domain 1(ED1), extra domain 2 (ED2), and extra domain 3 (ED3).

CD had a canonical TIM-barrel or (βα)8-barrel scaffold, comprising an interior of eight par allel β-strands in a barrel structure, surrounded by eight exterior α helices. ED1 showed a Rossmann-like α/β/α sandwich fold with three α-helices and five β-strands; ED2, an α + β protein fold with four α-helices and two β-strands; ED3, an all-α protein fold with seven α-helices. ED1 and ED2 were parallel to the TIM-barrel structure on each side, while ED3 lay on top of CD, resembling a cap . A metal ion, at the top central position of the TIM-barrel structure, was bound with the metal-coordination loop in the interface between CD and ED2 and a phosphate ion was covalently bound to Ser345 in the interface between CD and ED3. The zinc metal is essential to convert the substrate.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is [[UDP-galactose_4-epimerase]], which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.

This protein transforms an D-Tagaturonate into a D-Fructuronate and does the reverse reaction. The reaction first starts by the amino Asp159 deprotonating the C3′ OH group of D tagaturonate and generating an aldehyde group at C3′. Also in this step D-tagaturonate is cleaved into two three‑carbon catalytic intermediate molecules: 2-oxy-1-propene-1,3-diol and 2- hydroxy-3-oxopropanoate. During the electron movements, Zinc, the metal ion mentioned above, stabilizes the negatively charged oxygen atom at the C5′ position. The terminal aldehyde group of 2-hydroxy-3-oxopropanoate rotates to ward Glu126, and 2-oxy-1-propene-1,3-diol attacks the terminal aldehyde group of 2-hydroxy-3-oxopropanoate, which picks up the proton from the nearby Glu126 acid to complete the epimerization reaction.

As this protein is an epimerase, the same steps happen but in reverse order if the substrate is D-Fructuronate instead of D-Tagaturonate .

== Relevance ==

Carbohydrates are a major source of carbon and energy for all life forms. Xylan is a major component of hemicellulose and constitutes up to 35% of the total dry weight of woody plant tissues. Pectin is abundant in non-woody plant tissues and a structural heteropolysaccharide component of plant primary cell walls. Effective degradation and utilization of Xylan and Pectin can transform abundant agricultural waste materials into numerous valuable products, such as liquid fuels, solvents, food additives, and even medicinal products.

Pectin is easily and cheaply converted into a D-Glucuronate in a non reversible way by various pathways and Xylan is easily and cheaply converted into a D-Galacturonate in a non reversible way by various pathways. D-Glucuronate is transformed into D-Fructuronate in a reversible reaction into and D-Galacturonate is transformed into D-Tagaturonate, in an also reversible reaction. Both of these sugars have independent pathways to be transformed into molecules of interest. If one of them becomes a major source of substrate for a chemical reaction, with this epimerase, both of them can be used as feedstock, lowering the cost and increasing the application of this in places with a low availability of one feedstock but higher of the other. Or to arbitrage price diferences in those feedstocks given the limites supply of high volume and quality of Pectin/Xylan as a waste from other industries. This cost impact may impact on the economical viability of the process, making it competitive with regular non bio routes. Those bio routes usually have a better enviromental impact then the regular quimical ones.

<Structure load='6ILB' size='350' frame='true' align='right' caption='Epimerase scene='Insert optional scene name here' />

== References ==
<references/>

Fructuronate-tagaturonate epimerase

2022-06-26T21:31:19Z

Daniel Barzilay:

==Structure==

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
The structure comprises 490 amino acids, a metal ion and a phosphate ion. Each protomer consisted of four do mains: core domain (CD), extra domain 1(ED1), extra domain 2 (ED2), and extra domain 3 (ED3).

CD had a canonical TIM-barrel or (βα)8-barrel scaffold, comprising an interior of eight par allel β-strands in a barrel structure, surrounded by eight exterior α helices. ED1 showed a Rossmann-like α/β/α sandwich fold with three α-helices and five β-strands; ED2, an α + β protein fold with four α-helices and two β-strands; ED3, an all-α protein fold with seven α-helices. ED1 and ED2 were parallel to the TIM-barrel structure on each side, while ED3 lay on top of CD, resembling a cap . A metal ion, at the top central position of the TIM-barrel structure, was bound with the metal-coordination loop in the interface between CD and ED2 and a phosphate ion was covalently bound to Ser345 in the interface between CD and ED3. The zinc metal is essential to convert the substrate.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is [[UDP-galactose_4-epimerase]], which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.

This protein transforms an D-Tagaturonate into a D-Fructuronate and does the reverse reaction. The reaction first starts by the amino Asp159 deprotonating the C3′ OH group of D tagaturonate and generating an aldehyde group at C3′. Also in this step D-tagaturonate is cleaved into two three‑carbon catalytic intermediate molecules: 2-oxy-1-propene-1,3-diol and 2- hydroxy-3-oxopropanoate. During the electron movements, Zinc, the metal ion mentioned above, stabilizes the negatively charged oxygen atom at the C5′ position. The terminal aldehyde group of 2-hydroxy-3-oxopropanoate rotates to ward Glu126, and 2-oxy-1-propene-1,3-diol attacks the terminal aldehyde group of 2-hydroxy-3-oxopropanoate, which picks up the proton from the nearby Glu126 acid to complete the epimerization reaction.

As this protein is an epimerase, the same steps happen but in reverse order if the substrate is D-Fructuronate instead of D-Tagaturonate .

== Relevance ==

Carbohydrates are a major source of carbon and energy for all life forms. Xylan is a major component of hemicellulose and constitutes up to 35% of the total dry weight of woody plant tissues. Pectin is abundant in non-woody plant tissues and a structural heteropolysaccharide component of plant primary cell walls. Effective degradation and utilization of Xylan and Pectin can transform abundant agricultural waste materials into numerous valuable products, such as liquid fuels, solvents, food additives, and even medicinal products.

Pectin is easily and cheaply converted into a D-Glucuronate in a non reversible way by various pathways and Xylan is easily and cheaply converted into a D-Galacturonate in a non reversible way by various pathways. D-Glucuronate is transformed into D-Fructuronate in a reversible reaction into and D-Galacturonate is transformed into D-Tagaturonate, in an also reversible reaction. Both of these sugars have independent pathways to be transformed into molecules of interest. If one of them becomes a major source of substrate for a chemical reaction, with this epimerase, both of them can be used as feedstock, lowering the cost and increasing the application of this in places with a low availability of one feedstock but higher of the other. Or to arbitrage price diferences in those feedstocks given the limites supply of high volume and quality of Pectin/Xylan as a waste from other industries. This cost impact may impact on the economical viability of the process, making it competitive with regular non bio routes. Those bio routes usually have a better enviromental impact then the regular quimical ones.

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

Fructuronate-tagaturonate epimerase

2022-06-26T21:30:09Z

Daniel Barzilay:

==Structure==

<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
The structure comprises 490 amino acids, a metal ion and a phosphate ion. Each protomer consisted of four do mains: core domain (CD), extra domain 1(ED1), extra domain 2 (ED2), and extra domain 3 (ED3).

CD had a canonical TIM-barrel or (βα)8-barrel scaffold, comprising an interior of eight par allel β-strands in a barrel structure, surrounded by eight exterior α helices. ED1 showed a Rossmann-like α/β/α sandwich fold with three α-helices and five β-strands; ED2, an α + β protein fold with four α-helices and two β-strands; ED3, an all-α protein fold with seven α-helices. ED1 and ED2 were parallel to the TIM-barrel structure on each side, while ED3 lay on top of CD, resembling a cap . A metal ion, at the top central position of the TIM-barrel structure, was bound with the metal-coordination loop in the interface between CD and ED2 and a phosphate ion was covalently bound to Ser345 in the interface between CD and ED3. The zinc metal is essential to convert the substrate.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is [[UDP-galactose_4-epimerase]], which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.

This protein transforms an D-Tagaturonate into a D-Fructuronate and does the reverse reaction. The reaction first starts by the amino Asp159 deprotonating the C3′ OH group of D tagaturonate and generating an aldehyde group at C3′. Also in this step D-tagaturonate is cleaved into two three‑carbon catalytic intermediate molecules: 2-oxy-1-propene-1,3-diol and 2- hydroxy-3-oxopropanoate. During the electron movements, Zinc, the metal ion mentioned above, stabilizes the negatively charged oxygen atom at the C5′ position. The terminal aldehyde group of 2-hydroxy-3-oxopropanoate rotates to ward Glu126, and 2-oxy-1-propene-1,3-diol attacks the terminal aldehyde group of 2-hydroxy-3-oxopropanoate, which picks up the proton from the nearby Glu126 acid to complete the epimerization reaction.

As this protein is an epimerase, the same steps happen but in reverse order if the substrate is D-Fructuronate instead of D-Tagaturonate .

== Relevance ==

Carbohydrates are a major source of carbon and energy for all life forms. Xylan is a major component of hemicellulose and constitutes up to 35% of the total dry weight of woody plant tissues. Pectin is abundant in non-woody plant tissues and a structural heteropolysaccharide component of plant primary cell walls. Effective degradation and utilization of Xylan and Pectin can transform abundant agricultural waste materials into numerous valuable products, such as liquid fuels, solvents, food additives, and even medicinal products.

Pectin is easily and cheaply converted into a D-Glucuronate in a non reversible way by various pathways and Xylan is easily and cheaply converted into a D-Galacturonate in a non reversible way by various pathways. D-Glucuronate is transformed into D-Fructuronate in a reversible reaction into and D-Galacturonate is transformed into D-Tagaturonate, in an also reversible reaction. Both of these sugars have independent pathways to be transformed into molecules of interest. If one of them becomes a major source of substrate for a chemical reaction, with this epimerase, both of them can be used as feedstock, lowering the cost and increasing the application of this in places with a low availability of one feedstock but higher of the other. Or to arbitrage price diferences in those feedstocks given the limites supply of high volume and quality of Pectin/Xylan as a waste from other industries. This cost impact may impact on the economical viability of the process, making it competitive with regular non bio routes. Those bio routes usually have a better envrolment impact then the regular quimical ones.

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

Fructuronate-tagaturonate epimerase

2022-06-26T21:06:39Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-26T20:55:27Z

Daniel Barzilay:

File:Functionepira.png

2022-06-26T20:52:15Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-26T20:37:00Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-26T20:27:51Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-26T20:10:46Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-25T19:52:14Z

Daniel Barzilay:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Fructuronate-tagaturonate epimerase'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is [[UDP-galactose_4-epimerase]], which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.

== Relevance ==
Pectin is dadsada
Xylan is adasdsada

Pectin na dXylan is easiy conversed in tagaturonate and Pectin is easiy conversed in Fructuronate. To trasform easileyhas impact on...
== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

Fructuronate-tagaturonate epimerase

2022-06-25T19:51:48Z

Daniel Barzilay:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Fructuronate-tagaturonate epimerase'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is [[UDP-galactose_4-epimerase]], which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.
----

== Relevance ==
Pectin is dadsada
Xylan is adasdsada

Pectin na dXylan is easiy conversed in tagaturonate and Pectin is easiy conversed in Fructuronate. To trasform easileyhas impact on...
== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

Fructuronate-tagaturonate epimerase

2022-06-25T19:46:55Z

Daniel Barzilay:

==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Fructuronate-tagaturonate epimerase'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
Epimerases and racemases are isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules. Epimerases catalyze the stereochemical inversion of the configuration about an asymmetric carbon atom in a substrate having more than one center of asymmetry, thus interconverting epimers. One classical exemple of Epimerase is UDP-glucose 4-epimerase, which is used in the final step of galactose metabolism - catalyzing the reversible conversion of UDP-galactose to UDP-glucose.
----

== Relevance ==
Pectin is dadsada
Xylan is adasdsada

Pectin na dXylan is easiy conversed in tagaturonate and Pectin is easiy conversed in Fructuronate. To trasform easileyhas impact on...
== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

Fructuronate-tagaturonate epimerase

2022-06-25T19:41:08Z

Daniel Barzilay:

Fructuronate-tagaturonate epimerase

2022-06-25T19:34:43Z

Daniel Barzilay: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Fructuronate-tagaturonate epimerase'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

<Structure load='6ILB' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />