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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 of your Protein
The specific function of my protein is that it is an enzyme that comes from bacteria called Bacillus cereus. Its main function is to catalyze the chemical reaction by turning UDP-glucose into UDP- galactose in sugar-containing metabolites. It does this by flipping the chiral center. The PBD of this protein in 6ZLK and contains 3 ligands. The 3 ligands are UGB, NAD, and UGA. I am focusing on UGB. In our protein, the substrate and product bound enzymes to co-exist which creates an equilibrium structure. The product is UDP-GlcA.
the cofactor is the NAD+ which creates the product of UDP- GalA. The binding site is highlighted by a cluster of ordered waters, whose positions overlap the polar groups of the sugar substrate.
Our protein is pretty large and it's a great characteristic of a protein to be large because it determines whether the protein can interact with other molecules.
Biological relevance and broader implications
In the article that was assigned to me, they are studying the double nature of the enzymatic mechanism. Specifically at the active site and looking at the flexibility required for rotation. This is relevant because it helps us understand how the industrial applications of how enzymes work. Enzymes are used in the food industry quite often, They are used to manufacture dairy, meat, and bakery items. Understanding this protein can help us understand how its hydrophilic tendencies can impact the products it creates. This protein contains a few sugar rings in its metabolic pathway. The process creates sugar products. Studying Enzyme kinetics is important because enzymes are important to life. Understanding This information provides data about many diverse reactions, which helps us predict the metabolism of all living things. Even though changing Glucose into Galactose is a reaction near equilibrium and can be reserved because there isn't a big energy change, Studying this enzyme can help with biocatalysis. Biocatalysis is defined as the use of natural substances that include enzymes from biological sources or whole cells to speed up chemical reactions. In doing research on this enzyme-substrate complex it can help with improving the knowledge base of how catalysis impact reactions that include the production of alcohols from fermentation and cheese by the breakdown of proteins. The same types of enzymes that can be used in the food process, can be used in drug uptake. Enzymes often bind and act on their targets with great affinity and specificity. By looking at how a simple swing and flip of a pro-chiral 4-keto-hexose can change the molecule altogether and can change the whole structure and function of the protein. Second, enzymes are catalytic and convert multiple target molecules to the desired products, by adding different substrates and changing the formation of the structure, which can create many different products as we see in table 6 of our paper.
Important amino acids
Focussing on UGB ligand, Some important Amino acids would be Serine(128), Threonine(126), and Tyrosine(149) They are the catalytic amino acids in my enzyme.THR and TYR are Amphipathic. This means they have both hydrophilic and hydrophobic parts. Serine, Threonine, and Tyrosine are Polar. Polar hydrophilic amino acids are important in UGB ligand binding to the substrate. The interactions play an important role in "molecular recognition". Different polarity means that there is a different charge distribution among the amino acids. This becomes important for locating or identifying the accessible area to the substrate. I found that the rings on the end have a lot to do with binding. The key Amino acids for binding from the website and the article are Pro, Gly, and Arg. which you can also see in figure 2D. When I used the RCSB website I saw that the sugar rings were intertwined. These key amino acids are important because they participate in hydrogen bonding. The 4th carbon engages the residues in the triad. The 2nd carbon with the OH attached to it and the 3rd carbon with the OH is hydrogen-bonded to ARG-185 and PRO-85. The 5th carbon on the carboxylate interacts with the THr-126, Ser-127, and the Ser-128. With the hydrogen bonding happening at the site, the negative charges are what drive the strained backbone. The sugar cavity has 3 water in it and they overlap the 3’-OH,4’-OH, and 5’- carbonate groups. I also learned about disordered loops at the binding site. When You see the crystal structure through the X-ray. there is a blur and it means that the 2 loops are changing. So there ends up being no defined electron density. File:5244
Structural highlights
Our protein comes from the Bacillus cereus HuA2-4 organism. It includes the Epimerase domain. Our protein has a fair amount of secondary structures. These structures are important because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Our protein also consists of many Rossmann folds. This is a super secondary structure. It is composed of alternating alpha and beta sheets. The first Rossmann fold in a series is the one in contact with the nucleotide. In our protein, our nucleotide is the NAD. It contains a Rossmann folds that had 7 𝛃- strands and 6 𝜶-helices. The Rossman folds help stabilize the binding in the protein, which helps the catalytic triad have more efficient binding. This quaternary structure contains many hydrophobic interactions. This is true because of the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure. The subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains. Our protein is made up of two or more polypeptide chains. Our protein is a strong homodimer with a hydrophobic interaction face. This means that the amino acids at the binding sites have nonpolar R groups cluster together, on the inside of the protein. This leaves the hydrophilic amino acids on the outside of the structure.
The hydrophobic amino acids include THR, ILE, ALA, and PHE. This protein contains a few sugar rings in its metabolic pathway. The process creates sugar products. This enzyme creates a cavity where the sugar group binds and modifies itself. It has one Ramachandran Outlier. The paper also mentions the le loir pathway. This pathway is used in the catabolism of Galactose. [1]
Other important features
The enzyme prevents decarboxylation by keeping the CO2 on the structure. the structure of the apoenzyme together with the kinetic isotope, further outline the flexible loops. You can see this in scheme 1 where it breaks the double O bond on Carbon 4 and makes it alcohol and keeps the CO2 on the sugar structure. Another structural mechanism characteristic is that this protein has a lot of stacking. Hydrogen bond stacking benefits this protein by making it more structurally sound by helping the protein regulate electronegativity. You can see this on our protein in figure 2.A the block dotted lines are representing the hydrogen bonds in the structure. Figure 1 also shows that the crevice between the 2 domains encloses the active site. The crevice also denotes the hydrophobic interactions within the protein's 2 polypeptide faces. Hydrophobic interactions mean that the amino acids that have nonpolar r groups cluster together, on the inside of the protein. This leaves the hydrophilic amino acids on the outside of the structure. I saw a perfect example of this in figure 2. A, and 2.D. the protein we are studying contains F,Y, and L. Our protein also contains an enzyme-substrate complex. This is when an enzyme binds to the substrate and forms a complex. The result of the complex-forming causes the decrease in activation energy of the reaction and causes other ions and chemical groups to form covalent bonds creating additional steps in the process. This is shown in our protein in figure 7. In the presence of UDP-Glc, the enzyme closes over the substrate changing the position compared to the UDP- bound enzyme. There also is a C-terminal domain. whereas the smaller C-terminal domain provides the
the binding site for the UDP-GlcA substrate.
This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
- ↑ 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:https://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
![[1]](https://en.wikipedia.org/wiki/File:Leloir_pathway.png){kind=link}