Sandbox Reserved 1665: Difference between revisions

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<scene name='87/873227/Protein_view_2/2'>My protein is important for agricultural reasons, as you can see from the amazing ligand that is bound to it.</scene>
<scene name='87/873227/Protein_view_2/2'>My protein is important for agricultural reasons, as you can see from the amazing ligand that is bound to it.</scene>


The protein in the article is <scene name='87/873227/Cartoon_image_of_protein/5'>Aldehyde dehydrogenase (AldC)</scene> 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. In the article it states that the protein consists of 2 identical chains that are covalently bonded together known as a homodimer. Each chain of the protein consisted of two ligands, an NAD and an Octanal.
The protein in the article is <scene name='87/873227/Cartoon_image_of_protein/5'>Aldehyde dehydrogenase (AldC)</scene> 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.  
 
The organism that is affection the protein is called Pseudomonas syringae (PtoDC3000) which causing a mutation occurring in tomatoes.  




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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
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.
diverse bacterial virulence mechanisms to survive in the adverse environmental conditions of the phyllosphere.
 
 
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.


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.
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.
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== Important amino acids==
== Important amino acids==
'''4 Catalytic Residues''' <scene name='87/873227/4_catalytic_residues_tetrad/1'>(Tetrad)</scene> (green color)
'''4 Catalytic Residues''' (<scene name='87/873227/4_catalytic_residues/4'>Tetrad</scene>) (blue color)
:Asn 159, Glu 257, Gly 288, Cys 291(Cys 291 mutates to Ala 291)
:Asn 159, Glu 257, Gly 288, Cys 291(Cys 291 mutates to Ala 291)


The catalytic tetrad helps the protein by stabilizing and doing the reaction by using acid/base chemistry.
'''<scene name='87/873227/Nad_ligand/1'>NAD+ Ligand</scene>''' (binding site, <scene name='87/873227/Nad_binding_site/1'>19 residues</scene>)
 
'''<scene name='87/873227/Nad_ligand/1'>NAD+ Ligand</scene>''' (binding site, <scene name='87/873227/Nad_binding_site/2'>19 residues</scene>)
: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
: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


'''<scene name='87/873227/Octanol_ligand/1'>Octanal Ligand</scene>''' (<scene name='87/873227/Octanal-binding_site/2'>binding site</scene>)
'''<scene name='87/873227/Octanol_ligand/1'>Octanal Ligand</scene>''' <scene name='87/873227/Octanal-binding_site/1'>(binding site)</scene>
:Trp 160, Tyr 163, Trp 450, Phe 456, Tyr 458, Met 114, Leu 118  
:Trp 160, Tyr 163, Trp 450, Phe 456, Tyr 458, Met 114, Leu 118  
There were a couple of <scene name='87/873227/Intermolecular_forces/3'>intermolecular forces</scene> involved with the protein like <scene name='87/873227/Hydrophobic_interaction/2'>hydrophobic bonds</scene>, hydrogen bonds, polar interaction, <scene name='87/873227/Negatively_charged_acidic_bond/1'>negatively charged/ acidic bonds</scene>, and <scene name='87/873227/Positively_charged_basic/1'>positively charged/ basic bonds</scene>.


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.
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
https://proteopedia.org/wiki/images/3/3a/AldC_activie_sites.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.
 
Mutation in the NAD binding site occurred causing certain changes. Mutation in Lys 182 caused for there to be a removal of lysine side chained with a hydroxyl group in NAD binding site. K182A and K182Q show a lack of activity and a valine mutation (T234V) closely as well.


Mutation in the octanal binding site did occur and made certain changes as well. Asn 159, Trp 160, Ser 292, Leu 419, Phe 456 were the amino acids residues that got most disrupted. The reason behind this was that these amino acid residues were closer to the catalytic site of AldC than those other residues who receive a lesser disruption from the activity. From the table we can see as well N159 and L419 mutants lacked significant activity. 
(In the figure above it shows the active sites for AldC)
Red color indicated a <scene name='87/873227/Hydrophobic_interaction/1'>hydrophobic interaction</scene>
White color indicates a <scene name='87/873227/Polar_interaction/1'>polar interaction</scene>
Side chains interacting with Octanal are green
Side chains interacting with NAD are blue.
There are two water molecules (red spheres) interacting with the cofactor NAD
Hydrogen bonds interactions between amino acid residues and ligands are in yellow


== Structural highlights ==
== Structural highlights ==
<scene name='87/873227/Secondary_structure/4'>Secondary structure</scene> 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.
<scene name='87/873227/Secondary_structure/1'>Secondary structure</scene> 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 <scene name='87/873227/Space_filled_view/1'>space filled view</scene> of the protein it shows the intermolecular forces.


https://proteopedia.org/wiki/images/3/32/Aldehyde_dehydrogenage_of_AldC.PNG
https://proteopedia.org/wiki/images/3/32/Aldehyde_dehydrogenage_of_AldC.PNG
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