Enzyme Catalytic Mechanisms II Dr. Kevin Ahern

Protease Mechanisms Aspartic Acid Histidine Electron rich Metal Cysteine Electron rich Metal

Other Protease Families Cysteine Aspartyl Metallo- Papain Cathepsin D Carboxypeptidase A Cathepsin K Cathepsin E Collagenases Calpain Pepsin Caspase

Cysteine Proteases Substrate binding Sulfur anion Nucleophilic attack Bond breakage Peptide bond breakage Movement of proton Nucleophilic attack Release of first peptide Entry of water

Aspartyl Protease Substrate Aspartate side chains

Aspartyl Protease Mechanism of Action Nucleophilic attack Activation of water Aspartyl Protease Mechanism of Action Tetrahedral intermediate Breakage of peptide bond

CO2 + H2O ⇌ H2CO3 ⇌ HCO3- + H+ Carbonic Anydrase pH Activity 5.9 10,000 6.3 140,000 7.0 410,000 7.5 700,000 7.9 810,000 8.1 900,000 9.0 1,000,000

CO2 + H2O ⇌ H2CO3 ⇌ HCO3- + H+ ⇌ ⇌ ⇌ Carbonic Anydrase - - - HCO3- H2O ` HCO3- H2O + H+ C O = O H H H H H = - - O O CO2 O O C ⇌ ⇌ ⇌ - Zn+2 His O Zn+2 His Zn+2 His Zn+2 His

Restriction/modification Restriction Enzymes Bacterial defense Restriction/modification

Restriction Enzymes Hind III

Restriction Enzymes Cutting Mechanism

Electronic reorganization E = Glutamic acid D = Aspartic acid Activation of water Nucleophilic attack Magnesium ions Breakage of bond Electronic reorganization

Action of DNA methylase Restriction Enzymes Action of DNA methylase Me X

Metabolic Melody The Restriction Enzyme Song (to the tune of “Chim Chim Cher-ee”) Copyright © Kevin Ahern Metabolic Melody I'm obsessed with A-A-G-C-T-T Because it’s the binding site of Hin-d-III Cutting up DNA most readily The ends are not blunt when they’re cut up you see   Five prime overhangs of A-G-C-T Bacteria don’t have an immune system so They must fight off phages or they will not grow Protection by chopping is their strategy And one of the cutters we call Hin-d-III On binding to A-A-G-C-T-T The site recognition site’s bent easily Phosphodiester attacking meanwhile Has water behaving as nucleophile To stave off the phage for a little while Why don’t these enzymes cut cell DNAs? The answer’s provided by a methylase Adding a methyl group on top of what The sequence these enzymes would otherwise cut   So cells get protected in this simple way From nuclease chewing of their DNA The phage is not lucky in most every case Unless methylases win the enzyme race If that happens then, the cell gets erased