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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
My protein is important for agricultural reasons, as you can see from the amazing ligand that is bound to it.
The protein in the article is Aldehyde dehydrogenase (AldC) and It has many functions. It helps with detoxification of aldehydes which are highly reactive compounds that are generated through cellular metabolism. It is also involved in biochemical functions from ethanol metabolism through oxidations, polyamine metabolism, and protective cellular response to stresses. The organism that is affection the protein is called Pseudomonas syringae (PtoDC3000) which is a mutation occurring in tomatoes.
Biological relevance and broader implications
The plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. To suppress host defenses and promote diseases development, 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. In this case the plant pathogen is affecting tomatoes, causing a mutation in them where the tomatoes dont have any defensed to fight off this plant pathogen.
As mentioned in the article, there is a variety of pseudomonas species that have evolved to grow under unfavorable environmental conditions like for example sever nutrient limitations, extreme temperatures, high salinity, low oxygen or water availability. P. syringae, a species that includes many plant pathogenic strains, developed
diverse bacterial virulence mechanisms to survive in the adverse environmental conditions of the phyllosphere.
This can be relevant to certain famers growing crops in different environments or climates. Pseudomonas syringae is a pathogen that can attack a wide variety of woody plant, it especially attacks them when the plants have been damaged by frost or an injury. Knowing this information farmers can be prepared so their crops are not affected by this pathogen. They can use a certain type of spray/chemical to protect them from it.
Important amino acids
4 Catalytic Residues (Tetrad) (blue color)
- Asn 159, Glu 257, Gly 288, Cys 291(Cys 291 mutates to Ala 291)
NAD+ Ligand (binding site, 19 residues)
- Ile 155, Asn 159, Lys 182, Gly 219, Ile 233-Ser 236, Ala 239, Leu 242, Glu 257, Leu 258, Gly 259, Cys 291, Glu 391, Phe 393
Octanal Ligand (binding site)
- Trp 160, Tyr 163, Trp 450, Phe 456, Tyr 458, Met 114, Leu 118
There are a couple of intermolecular forces involved in the protein like hydrophobic bonds, hydrogen bonds, polar interactions, negatively charged/acidic interactions, and positively charged/ basic interactions.
In the article, there were other substrates mentioned that were detected in AldC by using spectrophotometric assay. Substrates that were identified were aliphatic aldehydes of 5–9-carbon length, like hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde. As substrates, octanal had the highest specific activity that function properly for AldC. The article also mentions that short 2–4-carbon aldehydes, branched aliphatic aldehydes, and larger aromatic aldehydes are poor substrates for AldC.
https://proteopedia.org/wiki/images/c/c9/AldC_Mutant_Site.PNG
In this table we can see how the organism Pseudomonas syringae is affecting the protein AldC by stopping enzyme activities in the protein. In the NAD ligand is stops enzyme activities for C291A and K182A and for the octanal substrate it stops enzyme activities for N159A and L419A.
Mutations in the NAD binding site occurred causing certain changes. Mutations in lys182 caused for there to be a removal of lysine side chained with a hydroxyl group in the NAD binding site. K182A and K182Q showed a lack of activity and a valine mutation (T234V) closely as well.
Mutations in the octanal binding site occurred as well and made certain changes to it. Asn 159, Trp 160, Ser 292, Leu 419, and Phe 456 were the amino acid residues that got most disrupted by the mutation. The reason behind this was that these amino acid residues were close to the catalytic cysteine site of AldC and those other residues received a lesser disruption from the activity. From the table above we can see N159 and L419 mutants lacked significant activity
Since the mutation occurred on Cys 291, we can see it caused a lack of activity between the two ligands NAD and Octanal in the protein.
Structural highlights
Secondary structure has feature and domains, the N-terminus of the protein contains a central Beta sheet that is surrounded by alpha helices to form the NAD(H)-binding site. Around the C-Terminus end of the protein it consists a mix of alpha/beta domains, which include a catalytic cysteine residue and forms the aldehyde -binding site. The article mentions as well what connects the N and C terminal domains of the protein AldC is by an interdomain linker region.
In this space filled view of the protein it show many amino acid residues that are hydrophobic (yellow) pushing away towards the binding sites because there are water molecules around them. Each chain of the protein shows a cleft for NAD and Octanal. We can tell there is a binding cleft for octanal because many amino residues like Trp 160, Tyr 163, Trp 450, Phe 456, and Tyr 468 provided a hydrophobic environment for this binding site.
https://proteopedia.org/wiki/images/3/32/Aldehyde_dehydrogenage_of_AldC.PNG
The enzyme functions primarily as a long-chained aliphatic aldehyde dehydrogenase.
The biochemical activity of AldC from PtoDC3000 is consistent with the traditional role of aldehyde dehydrogenases as metabolic clean-up enzymes that convert reactive aldehydes into less active carboxylates.
Other important features
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
