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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function(s) and Biological Relevance

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. ^[3]

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

This protein has a 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 also allows for visualization of different allosteric binding sites. This protein has a , called NSL. The structural fold of LsdA is that of a . 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 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 tertiary structure creates a 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 tertiary structure also creates a of Histidines to keep the iron molecule in place. This site is located in the active site where the single Fe2+ ion resides at the center of the β-propeller. This metal ion is coordinated in a tetragonal pyramidal fashion by four histidines (His-167, His-218, His-282, and His-472). 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

Phenylazophenol inhibits the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion. ^[4]