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DNA-bound AP Endonuclease (APE1) - DNA Repair

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DNA-bound AP Endonuclease (APE1) - DNA Repair

Postby paperclip » Sun Aug 21, 2005 9:19 am

This is odd.

Asp 210 acting as a Lewis base in the active site causes deprotonation of water creating a hydroxyl ion that acts as a nucleophile attacking the phosphate group resulting in cleavage of the scissile P-O3' bond.

Isn't Aspartate acidic and water relatively basic?
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Postby sdekivit » Sun Aug 21, 2005 9:30 am

in physiologic environment, aspartate is basic ;). it's restgroup is COO(-) ;) (pKa = 3,9) --> it can deprotonate a watermolecule. Because it has a free electrone pair, aspartic acid in physiologic envirnoment it can donate its electron pair and thus being a Lewis base
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Postby EmmVeePee » Sun Aug 21, 2005 2:51 pm

I had a lot to learn :?
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Postby paperclip » Mon Aug 22, 2005 7:56 am

Perhaps we can take Ka to mean how many times the acid flips between the two states of acid and base per second. Then can we make the reaction take place more readily?
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