[Nescafe]

Hi,

Let's say we are discussing phosphatases and the rate at which they dephosphorylate tyrosine residues. In most studies I see the unit for the rate of dephosphorylation to be reported in the units of s^-1 which makes me assume it is a first order rate constant. So does this mean that the rate = k [pTyr]? What about the fact that the mechanism of dephosphorylation involves a nucleophilic attack by a cysteine residue? I mean when the substrate enters the phosphatase binding pocket and sits in it comfortably it is attacked by a thiolate ion. This is I believe the rate determining step which if I am correct would be bimolecular and so rate = k [Enzyme-SH][pTyr] just like any SN2 reaction. I am having a hard time plotting my question but I am a bit confused when one say the rate of enzyme reaction, is it the rate pTyr -> Tyr + ATP which is rate= k[pTyr] or the rate at which the mechanism happens?

Hmmm running around in circles.

Nescafe.

[Yggdrasil]

It's hard to say what's happening without a context for the numbers you report, but enzymologists often report a number called k_cat for their enzymes.  This number, also referred to as the turnover number, is the rate of reaction at saturating enzyme concentration.  Because the concentration of enzyme is so high, enzyme-substrate binding is rapid and the rate limiting step of the reaction becomes the catalytic step (or some other step between binding of the enzyme and release of the product, such as a conformational change preceding or following catalysis).

[Faris Salama]

Hi

I think that you have to use the michaelis-menten equation to solve your problem. when we deal with protein it is not simple as SN1 and SN2 mechanisms, you need you need to consider the Involvement of the protein in the overall mechanism.

http://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics

Good luck
Faris   

[Babcock_Hall]

Most enzyme-catalyzed reactions are first-order with respect to [E], but they change over from being first order in substrate to zero-order in substrate as one raises the substrate concentration from below K_m to above it.  k_cat refers to saturating conditions, where [ S] >> K_m, but k_cat/K_m is another important kinetic values that refers to conditions where [ S] << K_m.  The units of k_cat/K_m are M^-1 s^-1.

With respect to protein tyrosine phosphatases, there is one (VHR phosphatase) for which the first half-reaction is rate-limiting, but if one mutates a particular residue, then the second half-reaction becomes rate limiting.  ATP is not a substrate for PTPases, BTW.