Fructuronate-tagaturonate epimerase
StructureStructure
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. FunctionEpimerases 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 .
RelevanceCarbohydrates 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 highlightsThis is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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ReferencesReferences
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