Can E.coli DNA Ligase Mimic Topoisomerase Activity with AMP?

[whamola411]

1. A. E.coli DNA ligase can act as a DNA gyrase in the presence of high concentrations of AMP. Explain.
B. Would you expect the E.coli ligase/AMP combination to resemble type I or II topoisomerase, or neither. Justify.
C. Would you expect human DNA ligase to act as a topoisomerase in the presence of high concentrations of AMP?

I know that human ligase uses ATP where ecoli ligase uses NAD+. For this reason, I feel that human ligase would be similar to a type II topoisomerase since it also uses ATP. For question A, I don't understand how AMP could be involved, since it is normally forms NMP. My guess is that it simply can't use ATP, but if AMP is available, it can still use that as an energy source.
For question B, I would also expect a resemblance to a type II topoisomerase because of the AMP involvement.
For question C, I wouldn't expect human DNA ligase to act as a topoisomerase, since it is involved in filling in nucleotides, where topoisomerases break nucleotides.

Thanks for your help!

 

[epenguin]

OK you have to look at the mechanism of the ligase (in both directions). I actually had only ever heard or remembered the ATP one, but it goes through adenylylation of the protein and the AMP is then transferred to a 5'P of the DNA forming a pyrophposphate bond and then... . If a ligase uses NAD⁺ instead of ATP can you not imagine a mechanism with a lot in common?

 

[whamola411]

Are you referring to the mechanisms of topoisomerases and ligases being in common?

 

[epenguin]

I am not offhand very familiar with facts of the mechanisms of topoisomerases. I think the question can be answered just knowing the mechanism of ligase (which you can find e.g. on http://en.wikipedia.org/wiki/DNA_ligase) and thinking about the mechamism.

If the NMN is a problem for you, just think about enzymes using ATP and work out an answer for those.

In second place then a mechanism using NMN is fairly predictable and not very different.

 

[DeeNos]

I would like to provide a response to the content about the DNA ligase/ topoisomerase study.

Firstly, the statement that E.coli DNA ligase can act as a DNA gyrase in the presence of high concentrations of AMP is interesting. DNA gyrase is a type II topoisomerase that is involved in supercoiling and relaxation of DNA. Normally, E.coli DNA ligase uses NAD+ as an energy source for its ligation activity. However, in the presence of high concentrations of AMP, it is possible that the ligase can utilize AMP as an alternative energy source to carry out its activity. This could explain the observed DNA gyrase-like activity of E.coli DNA ligase in the presence of AMP.

Moving on to question B, I would expect the E.coli ligase/AMP combination to resemble a type II topoisomerase. This is because type II topoisomerases, including DNA gyrase, also use ATP as an energy source for their activity. Therefore, it is likely that the E.coli ligase, when using AMP as an energy source, would exhibit similar characteristics to a type II topoisomerase.

Regarding question C, I agree that it is unlikely for human DNA ligase to act as a topoisomerase in the presence of high concentrations of AMP. Human DNA ligase uses ATP as an energy source, and its main function is to seal nicks in DNA during DNA replication and repair. In contrast, topoisomerases are involved in breaking and rejoining DNA strands, a different function from DNA ligase. Therefore, the use of AMP as an energy source may not affect the activity of human DNA ligase in the same way as it does for E.coli DNA ligase.

In conclusion, this study highlights the potential flexibility and adaptability of enzymes under different conditions. It also emphasizes the importance of understanding the specific functions and mechanisms of enzymes in different organisms. Further research could provide more insights into the role of AMP in the activity of DNA ligase and its potential implications in DNA repair and replication processes.