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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
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.
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.
Important 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
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
The structure is made up of about 60% alpha helices and 30% beta sheets and 10% of other structures like water. The shape of this structure looks like its split in two bulbs with a narrow middle part, this is because it is a homodimer. . You can also find two ligands in each side of the structure.
This is a structure to highlight the ligand of the protein while everything else is transparent. This is to show the main structure while highlighting the interaction with the ligand.
The ligands that can be found in the structure are octanal and NAD+.
Other important features
NEED TO REWORD THIS
The secondary structure features and domains of the AldC monomer are similar to those of other aldehyde dehydrogenase family members
The C-terminal region consists of a mixed a/b domain, which includes the catalytic cysteine
residue and forms the aldehyde-binding site"
"The N-terminal Rossmann-fold domain contains a central b-sheet (b9-b8-b7-
b10-b11) surrounded by a-helices to form the NAD(H)-binding site"
