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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 enzyme is from a tomato plant. Ald-C is an aldehyde dehydrogenase which are known to preform many biological functions. This enzyme also functions as a long-chain aliphatic aldehyde dehydrogenase. It can detoxify highly reactive compounds such as aldehydes. In a plant they also help with cell wall ester biogenesis, and help plant when they feel "stress" such as dehydration or environmental changes.
Ald-c is also linked to many biochemical processes such as ethanol metabolism by oxidation of acetyl aldehyde into acetate (removing aldehyde), and polyamine metabolism. Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses.
Biological relevance and broader implications
The Pseudomonas syringae plant pathogen effects crops, it is relevant because farmers and people that work in the agriculture industry need to know of all the ways that their crops can get infected.
To suppress host defenses and promote diseases develop- ment, Pseudomonas syringae produces a variety of virulence factors, including phytohormones or chemical mimics of hormones, to manipulate hormone signaling in its host plants. P. syringae and many other plant-associated microbial pathogens can synthesize the major auxin indole-3-acetic acid (IAA), whose production is implicated in pathogen virulence.
Pseudomonas syringae can destroy many different plants in different environments and temperatures, it can also survive and spread through the leaves. IAA (Indole-3-Acetic Acid) is a main plant hormone that is produced in the apical bud of and young leaves of plants and is known to be an inducer of cell division and elongation. IAA is often used in horticulture to promote adventitious root growth and are used commercially to create root stem cuttings and to promote uniform fruit and flowering growth.
This research is relevant to more areas in science because if someone want to make a defense chemical for Pseudomonas syringae they can use the chemistry in this paper to do so. There is a lost of valuable information that shows the chemistry, such as binding affinity. If someone is thinking about making a cure against Pseudomonas syringae they will need to know the characteristics of all the things that will bind well to it. This research paper also is useful in identifying superfamilies among different plant pathogens.
The genus Pseudomonas is one of the most ubiquitous and complex among the Gram-negative bacteria because many Pseudomonas species evolved to grow under unfavorable environmental conditions (i.e. severe nutrient limitation, extreme temperatures, high salinity, and low oxygen or water availability), they also evolved metabolic diversity and plasticity to use a variety of nutrient sources (i.e. carbon, nitrogen, and sulfur), to detoxify toxic organic chemicals, and to produce multiple specialized metabolites, including polymers and small molecule compounds.. PtoDC3000 uses several strategies to manipulate the auxin biology in its host plants to promote pathogenicity, including using an indole-3-acetaldehyde dehydrogenase for IAA synthesis. This states that it is quite difficult to treat this plant pathogen.
Important amino acids
There are which are essential for catalyzing the reactions and if one of them is mutated it can cause a huge effect in any enzyme. They are the ones that can preform acid base chemistry and catalyze the reaction which help it to make reactions happen appropriately.
there are which are NAD and OYA (octantal).
Cystine is an important amino acid but it was mutated to an alanine, which has possibly prevented the formation of a disulfide bridge.
The mutation was caused in the 291 position which is also one go the 4 catalytic residues. It was mutated to an alanine.
there are also other residues that are important for NAD binding.
Structural highlights
The octantal was the best substrate with the lowest Km and the highest affinity out of all 23 substrates.
Ald-C is also a homodimer. The central beta sheets are surrounded by alpha helices to form the NAD(H) binding site. The C terminal region has a mixture of both alpha and betta domain, which includes the catalytic cysteine residue and forms the aldehyde – binding site.Due to the mutated cystine to an alanine there may have been a disturbance in a potential disulfides bridge that happens between 2 cysteines and are essential for stability (). In this space fill scene you can see where the hydrogen bonds are. For the of Ald-C the alpha helices and beta sheets are shown
Other important features
Alanine substitutions of Glu 257 and Glu 391 severely disrupted AldC activity, showing that alanine had serious effects on other amino acids found along Ald-C. In contrast to the NAD(H)-binding site, apolar interactions dominate the octanal binding in the substrate- binding pocket. A cluster of aromatic residues and two apolar residues provide the hydrophobic environment that accommodates octanal and other aliphatic aldehydes. As described for other aldehyde dehydrogenase, the substrate-binding site forms an for adaptable apolar ligand interaction.
two apolar residues provide the hydrophobic environment that accommodates octanal and other aliphatic aldehydes. In the AldC crystal structure, Phe456 with Tyr468, which forms an interaction network with Tyr163 and Trp450.
Large structures are important because
