Oops, you meant catalytic residue. Check the following: Harris TK & Turner GJ Structural basis of pertubed pKa values of catalytic groups in enzyme active sites IUBMB life, 53 85-98 (Feb 2002)
Thierry ________________________________ From: Fischmann, Thierry Sent: Tuesday, February 07, 2012 10:59 AM To: 'Xiaodi Yu'; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] On pKa of Aspartic acid Check this review, for instance: Pace, C. et al. Protein Ionizable Groups: pK values and Their Contribution to Protein Stability and Solubility. J. Biol Chem. 284, 13285-13289 (May 15, 2009) Thierry ________________________________ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiaodi Yu Sent: Tuesday, February 07, 2012 10:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] On pKa of Aspartic acid Hi Deepak: I think it is common for the residues which participate catalysis to have a Pka deviated from the reality pKa value especially for acid/base catalysis (acid base titration assay can help you to figure out the way of catalysis). Usually the pKa values of these kind of critical residues are affected by their local environment and this character is related to the enzyme's working mechanism. I am sorry that I am not professional in enzyme, I cannot answer your questions for each questions. Yu Xiaodi ________________________________ Date: Tue, 7 Feb 2012 19:48:26 +0800 From: deepos...@gmail.com Subject: [ccp4bb] On pKa of Aspartic acid To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, We have solved the crystal structure of a human enzyme. The pKa of a catalytically critical aspartic acid has increased to 6.44. It is hydrogen bonded (2.8 Angstroms) to a water molecule that is supposed to donate a proton during the catalysis. Can anybody help me a) interpret the significance of this increase in pKa of the aspartic acid from 3.8 to 6.44 in context with the catalysis? Is this advantageous or detrimental? b) How is pKa related to an amino acids' ability to force a water molecule to donate a proton? c) At pH 7.4, the aspartic acid would be de-protonated irrespective of whether the pKa is 3.8 or 6.44; isn't that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
