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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
https://proteopedia.org/wiki/images/7/7f/Screen_Shot_2021-04-18_at_1.10.57_PM.png
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. Spinning protein
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
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 Catalytic Tetrad consisting of Asn159, Glu257, Gly288, and Cys291. Cys291 can be found to be mutated to an Ala Mutated Catalytic Tetrad
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 NAD and Octanal
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.
C291A mutation with ligand
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.Cartoon Secondary Structure Ribbon Protein Structure
Other important features
- ↑ 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
