*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
That is an excellent explanation, especially as the (much) higher reactivity of amides v. esters doesn't necessarily fully explain the faster hydrolysis of ester bonds (compared to amide bonds) by serine proteases. The idea of a greater tolerance for slight mis-positioning of the scissile bond for catalyzed cleavage of esters is interesting. In our recent JBC paper we have some crystallographic evidence which suggests (with plenty of caveats) that the scissile peptide bond may undergo a trans-cis isomerisation upon binding to a serine protease. The fact that the energy barrier for this isomerisation is much lower for esters (the thermodynamically favoured (Z)-conformation for esters is analogous to a trans-amide bond) may be an additional factor in the faster rate of hydrolysis. Best regards, Rupert Rupert Wilmouth School of Biological Sciences Nanyang Technological University ________________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Radisky, Evette S. Ph.D. Sent: 14 July 2006 01:17 To: Mark Matthewson; [email protected] Subject: RE: [ccp4bb]: structural basis for amide vs ester hydrolysis? I presume you are asking about serine proteases vs. serine esterases, which are both serine hydrolases and act via analogous mechanisms involving acyl-enzyme formation. Cleavage of the amide or peptide bond is the chemically more difficult reaction; cleavage of ester bonds occurs more readily (e.g. when comparing rates of spontaneous, uncatalyzed reactions), so proteases are evolved to carry out a more difficult job. For serine proteases, binding energy from favorable interactions at multiple sub-sites (especially P1, P2, P3, P4 subsites) is harnessed and translated directly into accelleration of kcat for the acylation step of the reaction, most likely through very precise positioning of the scissile peptide bond relative to the serine nucleophile. For shorter amide substrates, where the enzyme can't use to advantage the contacts of the extended substrate binding site, acylation tends to be slow and rate-limiting, and catalysis is actually faster for analogous ester sub! strates, indicating greater tolerance for slight mis-positioning of the scissile bond for catalyzed cleavage of esters. Hence, I would speculate that the evolutionary pressures on esterases have resulted in a family of hydrolases that do the intended job just fine, but do not have the precision of substrate positioning that would be required for cleavage of an analogous amide bond on a similar timescale. Cheers, Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-2857 (lab) ________________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Matthewson Sent: Thursday, July 13, 2006 12:05 PM To: [email protected] Subject: [ccp4bb]: structural basis for amide vs ester hydrolysis? Hi folks, I was puzzled as I went through the literature and could not find out why many esterases cannot catalyze the cleavage of an amide bond, while proteases can hydrolyze esters. Is there a structural basis why an esterase cannot hydrolyze an amide or peptide? Would greatly appreciate your expertise and help. Best regards, Rick ________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail Beta.
