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Function of your protein
This protein can be found in the plant pathogenic microbe Pseudomonas syringae strain PtoDC3000. The p. syringae mutautes its host, which in this case is tomato. The p. syringae produces a toxin that cause the tomato to not be able to fight off, there for causing diseases in the tomato. The research focuses on aldehyde dehydrogenases specifically aldC. aldehyde dehydrogenases are known for its capability to detoxing aldehydes, this is important because aldehydes are very reactive, so for an example from the article they can be turned into carboxylic acids which are not as reactive, which I believe slows down the mutation. The substrate of the AldC PtoDC3000 shows that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. This article states that they ran tests to find the best substrate for this enzyme, which they found multiple substrate such as aliphatic aldehydes of 5–9-carbon length, as well as hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde but it shows that octanal has the highest activity. This protein structure is a homodimer meaning it is two identical chains (A and B) covalently bonded together. the article states that there are still blurry areas to why the bacteria is able to grow on the plant in normal conditions rather than its preferred severe conditions. They continue their research to find these answers but there aren't any definitive answers now.
Biological relevance and broader implications
Learning about the mutant and its host is relevant because it can affect the food supply, which as humans we need. Studying this mutant will give us an understanding on what the mutation is and if it can be avoided. This research can lead the farming industry to a solution to the mutant. There are many chemicals that can be found being used with crops such as weed killers and fertilizers. The study of this helps humans be able to have a more abundant food supply that is disease and mutant free. This was also studied to get a better understanding of the p. syringae mutations and how to inhibit the tomatoes abilities to grow. The article states they didn't run any inhibitory trials but their research should be able to guide further research about this topic.
Important amino acids
The binding site of the protein consists of two ligands NAD+ and octanal, each made up different amino acids.
NAD+ binding site has 19 catalytic residues which consist of Ile155–Asn159, Lys182, Gly219, Ile233–Ser236, Ala239, Leu242, Glu257, Leu258, Gly259, Cys291, Glu391, and Phe393
Octanal Binding site has Trp160, Tyr163, Trp450, Phe456, and Tyr468 which are all aromatic and, the amino acids create a binding site that the article refers to as the aromatic box. It also has two other apolar residues Met114 and Leu118.
4 catalytic amino acids known as the consisting of Asn159, Glu257, Gly288, and Cys291. Cys291 can be found to be mutated to an Ala
The residues that were affected the most if mutated were mutations of Asn159, Trp160, Ser292, Leu419, and Phe456, this is because they are located closely to the protein active site.
There are two ligands in each of the chains in the homodimer
The mutation of C291A can be found in the middle of the two ligands affecting the binding efficiency of the structure. cysteine at position 291 is the most important amino acid of this structure. When it was mutated the protein had no activity compared to the other mutations.
Structural highlights
Secondary structure of this protein shows there is alpha helix and beta sheets at the C-terminus and only beta sheets in the N-terminus.
Each of the chains has 19 alpha helices, and 20 beta sheets, for a total of 38 alpha helices and 40 beta sheets.
Tertiary structure of the protein, showing only chain B of the protein.
Spacefill view of protein shows clearly the protein is a homodimer, it looks like it is two chains back to back with the binding site facing outwards. The color are there to represent the charges on the protein, red for negatively charged amino acids and blue for positively charged. This view also shows the quaternary structure of the protein which is the two chains together.
Other important features
The aromatic box consists of Trp160, Tyr163, Trp450, Phe456, and Tyr468. The amino acids provide a hydrophobic pocket that is needed for binding the octanal ligand becasue it requires a hydrophobic environment. These residues provide pi stacking to stabilize the structure . Mutations to these residues affected the efficiency of the octanal but it wasn't too significant, meaning the protein was still able to function with the mutations, its binding ability was not effected.
The nicotinamide ring is held by Van Der Waals interactions using the residues Leu258, Leu419, and Phe456 and is also hydrogen bonded by Leu258. The nicotinamide helps stabilize the NAD+ through these interactions,and a hydrogen bond to water.
