Sandbox Reserved 1559

2019-11-29T21:34:46Z

Robin Fenton:

{{Sandbox_Reserved_BHall_Chem351_F19}}
==Overview==
<StructureSection load='6ojt' size='440' side='right' frame='true' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. 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(s) and Biological Relevance ==
Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium ''Sphingomonas paucimobilis'' TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. LsdA has greatest substrate specificity for lignostilbene. The substrate's 4-hudryoxy moiety is required for catalysis. Phenylazophenol inhibits the cleavage of lignostilbene by LsdA. The breaking down of lignin is essential to the sustainable biorefining of lignocellulose. It is of great relevance to transforming lignocellulose to biofuels.

[[Image:lignostilbene.png]] [[Image:vanillin.png]]
== Broader Implications ==
Lignin represents 30% of the lignocellulose biomass. It consists of different aromatic building blocks, phenylpropanoids, which are extremely useful. Normally aromatic compounds are extracted from petroleum and are used to manufacture drugs, paint, plastics, etc. Therefore the potential of lignin is very high. Lignin is the most abundant polymer in nature other than cellulose and chitin, and it is the only one that contains such a large number of aromatic compounds.

== Structural highlights and structure-function relationships ==
The <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> of the <scene name='82/823083/Nsl_ligand/1'>NSL ligand</scene> consists of Phenylalanine59, Tyrosine101, and Lysine134.

The flat surface of the B-sheet is pushing the amino acids up, making it possible for the <scene name='82/823083/6ojttriad/1'>catalytic triad</scene> Phe59, Tyr101, and Lys134 to create interactions with the <scene name='82/823083/Nsl_ligand/1'>ligand</scene>.

[[Image:6ojtsecondarystructure.png|600 px]]

The tertiary structure creates a<scene name='82/823083/Aminobindingpocket/1'> binding pocket of amino acids</scene> that are important to the active site. His282 provides pi-stacking, Phe305 provides Hydrophobic contacts, and Tyr101 provides Hydrogen bonding. The tertiary structure also allows the NSL ligand to interact using its 4-hydroxy with the catalytic triad. LsdA can only cleave 4-hydroxystilbenes. The photo below shows the NSL ligand interacting in the binding pocket.

[[Image:NSL_ligand.png|600 px]]

The tertiary structure also creates a metal binding site of Histidines to keep the iron molecule in place. There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.

[[Image:Fe_View.png|600 px]]

== Energy Transformation ==

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/>

File:Fe View.png

2019-11-29T21:33:37Z

Robin Fenton: uploaded a new version of "Image:Fe View.png"

Sandbox Reserved 1559

2019-11-29T21:33:06Z

Robin Fenton:

{{Sandbox_Reserved_BHall_Chem351_F19}}
==Overview==
<StructureSection load='6ojt' size='440' side='right' frame='true' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. 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(s) and Biological Relevance ==
Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium ''Sphingomonas paucimobilis'' TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. LsdA has greatest substrate specificity for lignostilbene. The substrate's 4-hudryoxy moiety is required for catalysis. Phenylazophenol inhibits the cleavage of lignostilbene by LsdA. The breaking down of lignin is essential to the sustainable biorefining of lignocellulose. It is of great relevance to transforming lignocellulose to biofuels.

[[Image:lignostilbene.png]] [[Image:vanillin.png]]
== Broader Implications ==
Lignin represents 30% of the lignocellulose biomass. It consists of different aromatic building blocks, phenylpropanoids, which are extremely useful. Normally aromatic compounds are extracted from petroleum and are used to manufacture drugs, paint, plastics, etc. Therefore the potential of lignin is very high. Lignin is the most abundant polymer in nature other than cellulose and chitin, and it is the only one that contains such a large number of aromatic compounds.

== Structural highlights and structure-function relationships ==
The <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> of the <scene name='82/823083/Nsl_ligand/1'>NSL ligand</scene> consists of Phenylalanine59, Tyrosine101, and Lysine134.

The flat surface of the B-sheet is pushing the amino acids up, making it possible for the <scene name='82/823083/6ojttriad/1'>catalytic triad</scene> Phe59, Tyr101, and Lys134 to create interactions with the <scene name='82/823083/Nsl_ligand/1'>ligand</scene>.

[[Image:6ojtsecondarystructure.png|600 px]]

The tertiary structure creates a<scene name='82/823083/Aminobindingpocket/1'> binding pocket of amino acids</scene> that are important to the active site. His282 provides pi-stacking, Phe305 provides Hydrophobic contacts, and Tyr101 provides Hydrogen bonding. The tertiary structure also allows the NSL ligand to interact using its 4-hydroxy with the catalytic triad. LsdA can only cleave 4-hydroxystilbenes. The photo below shows the NSL ligand interacting in the binding pocket.

[[Image:NSL_ligand.png|600 px]]

The tertiary structure also creates a metal binding site of Histidines to keep the iron molecule in place. There have been two mechanisms proposed for Lsd's. In one mechanism, the hydroxystillbenoid is activated via the enzyme-catalyzed deprotonation of the 4-hydroxy group, which then allows electron delocalization toward an Fe3+. In the other mechanism, π electron density from the double bond is redistributed to the iron-oxy complex to form an Fe2+ cation intermediate. Deprotonation of the hydroxyl is demanding for both mechanisms and is assisted by Lys134 and Tyr101.

== Energy Transformation ==

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/>

File:FEView.png

2019-11-29T21:31:23Z

Robin Fenton:

File:Fe View.png

2019-11-29T21:29:45Z

Robin Fenton:

Sandbox Reserved 1559

2019-11-29T21:28:50Z

2019-11-29T17:36:17Z

Robin Fenton:

Sandbox Reserved 1559

2019-11-29T17:35:33Z

Robin Fenton:

{{Sandbox_Reserved_BHall_Chem351_F19}}
==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='6ojt' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. 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(s) and Biological Relevance ==
Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium ''Sphingomonas paucimobilis'' TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. LsdA has greatest substrate specificity for lignostilbene. The substrate's 4-hudryoxy moiety is required for catalysis. Phenylazophenol inhibits the cleavage of lignostilbene by LsdA. The breaking down of lignin is essential to the sustainable biorefining of lignocellulose. It is of great relevance to transforming lignocellulose to biofuels.

[[Image:lignostilbene.png]] [[Image:vanillin.png]]
== Broader Implications ==
Lignin represents 30% of the lignocellulose biomass. It consists of different aromatic building blocks, phenylpropanoids, which are extremely useful. Normally aromatic compounds are extracted from petroleum and are used to manufacture drugs, paint, plastics, etc. Therefore the potential of lignin is very high. Lignin is the most abundant polymer in nature other than cellulose and chitin, and it is the only one that contains such a large number of aromatic compounds.

== Structural highlights and structure-function relationships ==
The flat surface of the B-sheet is pushing the amino acids up, making it possible for the catalytic triad Phe59, Tyr101, and Lys134 to create interactions with the ligand.
[[Image:secondarystructure6ojt.png]]

== Energy Transformation ==

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/>

File:SecondaryStructure6ojt.png

2019-11-29T17:34:35Z

Robin Fenton: Secondary Structure of 6ojt

Secondary Structure of 6ojt