Ubiquitination of Proteins and Protein Degradation

Summary

This video explains the process of ubiquitination, where a ubiquitin protein is covalently linked to a lysine residue of target proteins. The purpose of ubiquitination is to tag proteins for degradation, especially misfolded or unnecessary proteins, by marking them for destruction by proteasomes. The video describes the role of enzymes E1, E2, and E3 in the ubiquitination process, and explains how the tagged proteins are degraded by proteasomes into peptides. Additionally, it mentions prions, which resist degradation by proteasomes. Viewers are encouraged to like and subscribe for more content.

Takeaways

• 🔗 Ubiquitination is the process where ubiquitin proteins are covalently linked to lysine residues of target proteins.
• 🔬 Ubiquitination marks proteins for destruction or degradation, particularly misfolded, toxic, or unnecessary proteins.
• ⚙️ Ubiquitination is also involved in some signaling pathways, helping switch them on or off by degrading proteins.
• ⚡ The ubiquitination process is initiated by three types of enzymes: E1 (activating enzyme), E2 (conjugating enzyme), and E3 (ligase enzyme).
• 💡 E1 enzyme activates ubiquitin by forming a thioester bond between ubiquitin and itself, in an ATP-dependent process.
• 🔄 E2 enzyme transfers the activated ubiquitin from the E1 enzyme to its own cysteine residue.
• 🎯 E3 enzyme facilitates the transfer of ubiquitin from E2 to the lysine residue of the target protein, forming an isopeptide bond.
• 📏 Proteins can be mono-, multi-, or poly-ubiquitinated depending on the number of ubiquitin molecules attached.
• 🏭 The degradation of ubiquitinated proteins is carried out by proteasomes, particularly the 26S proteasome, which consists of 20S proteasome and 19S caps.
• 🧩 Proteasomes break down the tagged proteins into short peptides, recycling ubiquitin in the process.

Q & A

What is ubiquitination?

Ubiquitination is a biochemical process in which a ubiquitin protein is covalently linked to the lysine residue of target proteins. This process often tags proteins for degradation.

What type of bond is formed between ubiquitin and the lysine residue of the target protein?

An isopeptide bond is formed between the lysine residue of the target protein and ubiquitin.

What is the purpose of ubiquitination?

The purpose of ubiquitination is to tag proteins for destruction or degradation, particularly proteins that are misfolded, toxic, or no longer needed by the cell. It can also play a role in regulating signaling pathways by degrading specific proteins.

What enzymes are involved in the ubiquitination process?

The enzymes involved in ubiquitination include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligase enzymes (E3).

What role does the E1 enzyme play in ubiquitination?

The E1 enzyme, also known as ubiquitin-activating enzyme, links itself with the carboxyl end of ubiquitin through a thioester bond. This step is energy-dependent and requires ATP.

How does the E2 enzyme contribute to ubiquitination?

The E2 enzyme, or ubiquitin-conjugating enzyme, transfers the activated ubiquitin from the E1 enzyme to its cysteine residue, preparing it for the next step in the process.

What is the function of the E3 enzyme in ubiquitination?

The E3 enzyme, or ubiquitin ligase, facilitates the transfer of ubiquitin from the E2 enzyme to the lysine residue of the target protein, forming an isopeptide bond between them.

What are the different types of ubiquitination?

Proteins can undergo mono-ubiquitination (single ubiquitin attachment), multi-ubiquitination (multiple ubiquitin molecules attached at different sites), or poly-ubiquitination (a chain of ubiquitins attached to a single lysine residue).

What is the structure of the proteasome, and how does it function in protein degradation?

The proteasome consists of two alpha rings and two beta rings, forming the 20S core particle. This core particle is capped by a 19S regulatory particle, forming the 26S proteasome. The proteasome recognizes ubiquitinated proteins, degrades them into peptides, and recycles the ubiquitin molecules.

What happens to prions during the degradation process?

Prions, which are misfolded proteins, are resistant to degradation by proteasomes. This makes them difficult to degrade, leading to the persistence of prion-related diseases.

Outlines

00:00

👋 Introduction to Ubiquitination

The video begins with an introduction to the concept of ubiquitination, explaining that it is a biochemical process where ubiquitin proteins are covalently linked to lysine residues of target proteins. This process, driven by enzymes, tags proteins for degradation. Ubiquitination mainly occurs in proteins that are misfolded, toxic, or no longer useful to the cell. Additionally, it plays a role in regulating signaling pathways by marking proteins for destruction. The video briefly touches on how this tagging leads to protein degradation through the action of proteasomes, a topic that will be discussed further.

🔧 Enzymes Driving Ubiquitination

The discussion then shifts to the enzymes involved in ubiquitination. There are three key enzymes: E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin ligase). The E1 enzyme binds to the ubiquitin protein through a thioester bond, a process requiring ATP. The activated ubiquitin is then transferred to the cysteine residue of E2. Finally, E3 transfers the ubiquitin from E2 to the target protein, marking it for degradation. This section explains the step-by-step role of these enzymes in facilitating the ubiquitination process.

🔄 Detailed Mechanism of Ubiquitination

A more detailed explanation of the ubiquitination mechanism is provided in this section. Ubiquitin, activated by the E1 enzyme, is transferred to E2 and ultimately conjugated to the target protein by E3 ligase. The bond formed between the lysine residue of the target protein and the ubiquitin is an isopeptide bond. The target protein can be tagged with one or multiple ubiquitins (mono- or poly-ubiquitination). The ubiquitinated protein is now ready for degradation by proteasomes.

🧬 Structure and Function of Proteasomes

The proteasome is described in detail, showing its structure with two alpha and two beta rings that form a core, referred to as the 20S proteasome. The 19S cap is attached to either one or both alpha rings, creating the fully functional 26S proteasome. The role of the 19S cap in recognizing ubiquitin-tagged proteins is highlighted. Once recognized, the protein is pulled into the proteasome and broken down into peptides, while the ubiquitin is recycled for future use.

🧩 Final Steps of Protein Degradation

This section wraps up the explanation of protein degradation by discussing how the proteasome breaks down ubiquitinated proteins into short peptides. It also mentions prions, which are misfolded proteins resistant to degradation by proteasomes. This resistance can lead to certain diseases. The video concludes with a brief recap of how ubiquitination tags proteins for degradation and how proteasomes carry out this degradation process.

👍 Conclusion and Call to Action

In the final part, the video wraps up by summarizing the key points discussed, focusing on the ubiquitination process and its role in protein degradation. The presenter encourages viewers to give a thumbs up if they enjoyed the video and to subscribe to the channel for more content.

Keywords

💡Ubiquitination

Ubiquitination is the biochemical process where ubiquitin, a small regulatory protein, is covalently attached to a lysine residue of a target protein. This process serves as a tagging mechanism to mark proteins for degradation. In the video, ubiquitination is central to the discussion, as it leads to the eventual breakdown of misfolded or unnecessary proteins in cells.

💡Proteins

Proteins are large, complex molecules that play many critical roles in biological systems. In the video, proteins are discussed in the context of their ubiquitination and degradation, focusing on those that are misfolded, toxic, or no longer needed by the cell.

💡Lysine Residue

Lysine residue refers to a specific amino acid within a protein that can form a covalent bond with ubiquitin during ubiquitination. In the video, the lysine residue of the target protein is the site where ubiquitin is attached, forming an isopeptide bond.

💡Isopeptide Bond

An isopeptide bond is a type of covalent bond formed between the ubiquitin protein and the lysine residue of the target protein. This bond is critical in the ubiquitination process and is discussed in the video as the mechanism through which proteins are tagged for degradation.

💡E1 Enzyme (Ubiquitin-activating enzyme)

The E1 enzyme is responsible for the activation of ubiquitin in an ATP-dependent process. It forms a thioester bond with ubiquitin, initiating the ubiquitination process. In the video, it is mentioned as the first step in the enzymatic process that leads to protein degradation.

💡E2 Enzyme (Ubiquitin-conjugating enzyme)

The E2 enzyme transfers activated ubiquitin from the E1 enzyme to itself through a cysteine residue. This enzyme is critical in the process of transferring ubiquitin to the target protein. The video explains how this transfer prepares ubiquitin for the final step in its attachment to the target protein.

💡E3 Ligase (Ubiquitin ligase)

The E3 ligase is the enzyme responsible for the final transfer of ubiquitin from the E2 enzyme to the target protein's lysine residue, completing the ubiquitination process. In the video, it is highlighted as the enzyme that ensures specificity, recognizing the protein that needs to be degraded.

💡Proteasome

The proteasome is a large protein complex responsible for degrading ubiquitinated proteins into smaller peptides. In the video, the 26S proteasome, composed of alpha and beta rings, is discussed as the cellular machine that recognizes ubiquitin-tagged proteins and carries out their degradation.

💡Prions

Prions are misfolded proteins that are resistant to proteolysis, meaning they cannot be easily degraded by proteasomes. In the video, prions are mentioned as an exception to normal protein degradation pathways, posing a challenge due to their resistance to standard cellular breakdown mechanisms.

💡ATP

ATP (adenosine triphosphate) is the energy currency of the cell, and it is required for the activation of ubiquitin by the E1 enzyme in the ubiquitination process. The video describes ATP as a necessary component for initiating the covalent bonding between ubiquitin and the target protein.

Highlights

Ubiquitination is a biochemical process where ubiquitin protein is covalently linked to the lysine residue of target proteins.

The bond formed between ubiquitin and the lysine residue of the target protein is an iso-peptide bond.

Ubiquitination marks or tags proteins for destruction or degradation, particularly misfolded, toxic, or unnecessary proteins in the cell.

Ubiquitination also plays a role in regulating signaling pathways by marking proteins for destruction, enabling the activation or deactivation of pathways.

Three main enzymes drive the ubiquitination process: E1 (activating enzyme), E2 (conjugating enzyme), and E3 (ligase enzyme).

E1 enzyme links with the carboxyl end of ubiquitin protein through a thioester bond in an ATP-dependent manner.

E2 enzyme transfers activated ubiquitin from the E1 enzyme to the cysteine residue of the E2 enzyme.

E3 ligase transfers ubiquitin from the E2 enzyme to the lysine residue of the target protein, forming an iso-peptide bond.

Proteins can undergo mono-ubiquitination, multi-ubiquitination, or poly-ubiquitination.

The degradation of ubiquitinated proteins occurs in the proteasome, a multi-subunit complex responsible for breaking down proteins into peptides.

The proteasome structure consists of two alpha rings and two beta rings sandwiched between the alpha rings, forming the 20S proteasome.

The fully functional 26S proteasome includes a 19S cap attached to either one or both alpha subunit rings of the 20S proteasome.

The 19S cap recognizes the ubiquitin chain on the tagged protein and guides it into the proteasome for degradation.

The ubiquitin proteins are recycled after degradation, and the target protein is broken down into short peptides.

Some misfolded proteins, like prions, resist degradation by proteasomes due to their structural properties.

Transcripts

oh hello friends in this video we'll be

discussing about ubiquitination of

proteins and also we'll be discussing

about protein degradation first of all

let's see what ubiquitination is it is

the biochemical process while ubiquitin

protein is covalently linked it to

lysine residue off target proteins if we

see it diagrammatically we see we have a

target protein like this as shown in the

figure and on the Left we have a

ubiquitin protein shown as a blue dot

and in this process of linking ubiquitin

with protein which is initiated by

enzymes and we get the ubiquitin

attached to it in this manner and it

must be noted here the bond between

lysine residue and the ubiquitin is the

iso peptide bond

so in nutshell we can say proteins are

getting tagged by you acute in protein

on their lysine residue but what's the

purpose of this ubiquitination the

purpose of ubiquitination is to mark or

tag the proteins for destruction or

degradation the ubiquitination

occurs on those proteins which are Mis

folded or toxic proteins or on those

proteins which are of no use in the cell

ubiquitination also happens to be part

of some signaling pathways in order to

switch on and switch off the pathways by

the destruction of proteins so we say

ubiquitination tags the proteins for

degradation and the rest of the work is

done by proteomes which we will see

later on in this video now let's jump

towards the enzymes first that drive the

ubiquitination process first of all we

have you acute in activating enzymes in

short we say it's even enzyme this even

enzyme links itself with the carboxyl

end of cuba cute in enzyme through

thirst or bond and this step is energy

dependent so it needs ATP's then we have

ubiquitin conjugating enzyme e 2 which

transfers the activated u Akutan from

even towards the cysteine residue of e 2

enzyme and finally we are you acute in

ligase enzyme called III enzyme whose

function is transfer the Ubiquiti into

that target protein

now let's see the mechanism of your

coordination process in detail the

structure of ubiquitin protein is shown

in the diagram

while we see you bruiting attach it to a

carboxyl and then to this the even

enzyme acts on it in presence of ATP and

in this relation the ubiquitin is linked

to the even enzyme as shown in the

structure by Pauling thioester bond with

even enzyme then e2 enzyme comes in and

transpose the activated u Akutan from

even towards the cysteine residue of e

to enzyme now the ubiquitin is

conjugated to the e2 enzyme and we have

a target protein which needs to be

tagged it with this ubiquitin protein so

finally the last enzyme that's III known

as ubiquitin ligase comes in and

transpose the ubiquitin from e2 towards

the lysine residue of target protein by

forming the ISO peptide bond between

lysine and Ubiquiti and also keep this

thing in mind the proteins can be mono

ubiquitinated Multi ubiquitinated or

even poly ubiquitinated so now we have

ubiquitinated protein ready to be

decorated and for this degradation

process we need protostomes if we see

the structure of proteasome we have two

alpha rings and also two bitter rings

which are sandwiched between alpha rings

as shown in the diagram this makes us

the 20s proteasome and to this 20s

proteasome the 19's cap is attached to

either one or both alpha subunit rings

and this completes the structure thus

forming as the 26s proteasome which is

fully functional to decorate the

proteins into peptides then the next

step of protein degradation will be

recognition and the Tiger protein is

recognized by 19's cap when it binds to

the ubiquitin chain and pushes the rest

of the protein into the proteasome

thus recycling back the ubiquitin

proteins and we get the target protein

converted into short peptides by the

action of proteome and also remember

that there are some proteins miss folded

proteins which are called prions which

need to be degraded but are not degraded

due to the

stens of prions for proteolysis by

protozoans

so this is all about ubiquitination of

proteins how ubiquitination of proteins

is done and how then proteins are

subjected to that degradation by

protostomes so this is all about it I

hope you liked the video if you liked it

give it a thumbs up and make sure to

subscribe this channel

Thanks