Sandbox Reserved 1559
From Proteopedia
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== Function(s) and Biological Relevance == | == Function(s) and Biological Relevance == | ||
| - | <scene name='82/823083/6ojt/1'>Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium ''Sphingomonas paucimobilis'' TMY1009</scene> 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- | + | <scene name='82/823083/6ojt/1'>Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium ''Sphingomonas paucimobilis'' TMY1009</scene> 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-hydryoxy 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.<ref> PMID:31292192 </ref> |
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== Structural highlights and structure-function relationships == | == Structural highlights and structure-function relationships == | ||
| - | This protein has a <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge). | + | This protein has a <scene name='82/823083/6ojttriad/1'>Catalytic Triad</scene> which consists of the amino acids Phe-59, Tyr101, and Lys-134. These amino acids play an important role in catalysis for the protein. Lys-134 proved to be the most important amino acid. The basic spacefill view of the entire protein allows for visualization of the different elements in different colors. The elements shown are carbon (Grey), nitrogen (Blue), and oxygen (Red). The <scene name='82/823083/Spacefill/1'>spacefill view</scene> also allows for visualization of different allosteric binding sites. This protein has a <scene name='82/823083/Nsl_ligand/1'>ligand</scene>, called NSL. The structural fold of LsdA is that of a <scene name='83/830391/Rainbow_7blade_beta_propeller/2'>seven-bladed β-propeller</scene>. <ref> PMID: 30115012 </ref> <scene name='82/823083/Hydrophobic/1'>Hydrophobic interactions</scene> are highlighted in grey, and polar regions are purple, while the ligand is yellow. This protein has a catalytic triad for binding that consists of tyrosine (hydrophilic), phenylalanine (hydrophobic), and lysine (has a positive charge). |
The <scene name='82/823083/Secondary_structure/1'>secondary structure</scene> of this protein is mostly composed of β-sheets with minimal areas of alpha-helices. Beta sheets provide a flat surface for interactions to occur. | The <scene name='82/823083/Secondary_structure/1'>secondary structure</scene> of this protein is mostly composed of β-sheets with minimal areas of alpha-helices. Beta sheets provide a flat surface for interactions to occur. | ||
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== Energy Transformation == | == Energy Transformation == | ||
| - | Phenylazophenol inhibits the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion. | + | Phenylazophenol inhibits the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion. |
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
| - | < | + | <references/> |
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| This Sandbox is Reserved from Aug 26 through Dec 12, 2019 for use in the course CHEM 351 Biochemistry taught by Bonnie_Hall at the Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1556 through Sandbox Reserved 1575. |
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD. Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase. J Biol Chem. 2019 Jul 10. pii: RA119.009428. doi: 10.1074/jbc.RA119.009428. PMID:31292192 doi:http://dx.doi.org/10.1074/jbc.RA119.009428
- ↑ Loewen PC, Switala J, Wells JP, Huang F, Zara AT, Allingham JS, Loewen MC. Structure and function of a lignostilbene-alpha,beta-dioxygenase orthologue from Pseudomonas brassicacearum. BMC Biochem. 2018 Aug 16;19(1):8. doi: 10.1186/s12858-018-0098-4. PMID:30115012 doi:http://dx.doi.org/10.1186/s12858-018-0098-4
