Sandbox Reserved 1671

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Revision as of 01:00, 19 April 2021

This Sandbox is Reserved from 01/25/2021 through 04/30/2021 for use in Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1665 through Sandbox Reserved 1682.

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Ald-C

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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.

1 Ald-C structure
2 Function of your protein
3 Biological relevance and broader implications
4 Important amino acids
5 Structural highlights
6 Other important features

Ald-C structure

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.

Biological relevance and broader implications

The Pseudomonas syringae pant 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. Pseudomonas syringae makes the plants defenses against pathogens weak and it is more susceptible to get sick, by producing many different virulence factors such as parahormones, which are chemicals that are similar to the plants natural hormones but are not. Pseudomonas syringae can destroy many different plants in different environments and temperatures, it can also survive and spread through the leaves.

This paper 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.

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).

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.

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. This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

Lee, S. G., Harline, K., Abar, O., Akadri, S. O., Bastian, A. G., Chen, H. S., Duan, M., Focht, C. M., Groziak, A. R., Kao, J., Kottapalli, J. S., Leong, M. C., Lin, J. J., Liu, R., Luo, J. E., Meyer, C. M., Mo, A. F., Pahng, S. H., Penna, V., Raciti, C. D., … Jez, J. M. (2020). The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase. The Journal of biological chemistry, 295(40), 13914–13926. https://doi.org/10.1074/jbc.RA120.014747

↑ 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:http://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

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Sandbox Reserved 1671

From Proteopedia

Revision as of 01:00, 19 April 2021

Ald-C

Contents

Ald-C structure

Function of your protein

Biological relevance and broader implications

Important amino acids

Structural highlights

Other important features

References

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@@ Line 32: / Line 32: @@
 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.
 == 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.
+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.
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.