Understanding Enzyme Efficiency: The Role of kcat and Km Values

[schordinger]

kcat/Km is representing the enzyme efficiency, isn't it?

however, if two enzyme have same value of kcat/Km, but if one of them have value of kcat smaller than the other, is they are really equally effective??

why not the smaller kcat enzyme have a lower efficiency ?

 

[Mike H]

So we have two different enzymes, A and B, both with the same value of kcat/KM. If let's say enzyme A has a higher value of kcat, then in order to have an equivalent ratio enzyme B must have an appreciably smaller value of KM. This means that enzyme B has an very strong affinity for its substrate and is not likely to be as promiscuous with its binding as enzyme A. So the decrease in one property of the enzyme has its slack taken up by its other property - so for enzyme A, its weaker affinity is made up by its higher turnover.

That's about as simple an explanation as I can offer.

 

[schordinger]

I see...
but could that two enzyme catalyze reaction at same rate?

or it is impossible to predict, with only knowing kcat/Km ?

actually, I am studying some kinetics of a modified enzyme, and found that the reaction proceed slower than original one, but the kcat/Km of the modified one is larger...

 

[Mike H]

There's nothing inherently preventing two enzymes from catalyziing their respective reactions at the same rate. My brain is shutting down on me right now, but I'm sure there have to be at least two different enzymes that catalyze their respective chemistry at the same rate. Someone else can do the favor of providing us with a specific example. :)

I'm confused - if you have kcat, why would you need to do any prediction? That number tells you the turnover of substrate into product per unit time (typically per second).

I would figure that your modified enzyme has a higher affinity (lower KM) then. Is that correct?

 

[schordinger]

"kcat/Km" of the two enzyme is indeed different...

Let me describe a bit more detial...

what I have done was comparing two modified enzymes, one of it (just call it enzyme A) has smaller kcat and Km value.
However, the kcat/Km is larger than the other (say, enzyme B).

Experimental data showed that reaction catalyzed by enzyme A is slower than enzyme B, even kcat/Km of A is larger than B...

that make me wonder what "kcat/Km" really means...
say, larger "kcat/Km" means more effective, what is "more effective" ?, just faster ? if so, it cannot explain my experimental data...(or my data have problem ^_^)...

 

[Mike H]

In some regard, kcat/KM is also a measure of the enzyme's substrate specificity, which is more nuanced of an idea than just efficiency. This connects both the affinity of the enzyme for the substrate as well as the rate at which the enzyme can actually do the chemistry.

What matters is the ratio of the two values. You can have an absurdly high kcat, but if the enzyme has only a weak affinity for the substrate (high KM), then it is not as efficient as an enzyme with a smaller kcat but a significantly smaller KM. In the first case, yes, the rate of reaction is very fast but the enzyme is not very specific in its substrate binding and so spends a good deal of time messing about with other substrates, and so is not very efficient. In the second case, the enzyme is far slower but spends more of its time working with the proper substrate. (Apologies for the slight anthropomorphization.)

So in your case, enzyme A may be slower, but its substrate affinity makes up for it so that most of the substrate which is bound is the proper substrate. Your enzyme B - which is faster but has a smaller kcat/KM - doesn't have as strong as an affinity and so doesn't work nearly as efficiently.

Is this starting to make sense now?

Must be off to lunch...