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Enzymes and Catalytic Mechanisms |
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1 | (68) |
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Catalysis and the Active Site |
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1 | (2) |
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Rate Enhancement in Enzymatic Catalysis |
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3 | (2) |
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Conformational Mobility in Catalysis |
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5 | (4) |
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Substrate-Induced Conformational Changes |
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5 | (1) |
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Catalysis of Multistep Reactions |
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6 | (1) |
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Structural Mobility in Enzymes |
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6 | (3) |
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9 | (7) |
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9 | (2) |
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Acid- and Base-Catalyzed Reactions |
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11 | (5) |
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16 | (5) |
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21 | (9) |
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21 | (2) |
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Imine Formation by Lysine |
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23 | (3) |
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26 | (4) |
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30 | (4) |
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Strong and Weak Hydrogen Bonds |
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30 | (2) |
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Hydrogen Bonding in Catalysis |
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32 | (2) |
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Binding Energy in Catalysis |
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34 | (19) |
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Binding and Activation Energy |
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34 | (2) |
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The Active Site as an Entropy Trap |
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36 | (4) |
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Dissecting the Binding Effect in Enzymatic Action |
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40 | (1) |
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Stabilization of the Transition State |
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41 | (5) |
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Binding the Near Attack Conformation |
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46 | (2) |
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Destabilization of Ground States |
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48 | (1) |
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Rate Enhancement through Binding of Remote Groups |
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48 | (5) |
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Characterization of Active Sites |
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53 | (9) |
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Competitive Inhibitors: Analogs of Substrates |
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53 | (1) |
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Group-Selective Chemical Modification |
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53 | (4) |
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Site-Directed Mutagenesis |
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57 | (2) |
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59 | (3) |
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Why Are Enzymes Large Molecules? |
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62 | (7) |
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Sizes of Enzymatic Binding Domains |
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62 | (1) |
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63 | (6) |
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Kinetics of Enzymatic Reactions |
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69 | (60) |
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69 | (22) |
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70 | (4) |
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74 | (15) |
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Three-Substrate Reactions |
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89 | (2) |
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91 | (10) |
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Classes of Isotope Effects |
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91 | (4) |
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Measurement of Isotope Effects |
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95 | (6) |
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101 | (10) |
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101 | (1) |
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102 | (9) |
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111 | (6) |
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111 | (1) |
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Measurements of pH-Rate Profiles |
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111 | (6) |
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117 | (12) |
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118 | (2) |
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Binding Equations for Cooperative Systems |
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120 | (3) |
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Aspartate Transcarbamoylase |
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123 | (6) |
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Coenzymes I: Organic Coenzymes |
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129 | (60) |
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129 | (12) |
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Structures and Functions of Nicotinamide Coenzymes |
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129 | (3) |
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Stereospecificity of Hydride Transfer |
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132 | (2) |
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134 | (7) |
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141 | (6) |
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141 | (1) |
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141 | (6) |
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147 | (1) |
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148 | (10) |
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Enzymatic Reactions Facilitated by Pyridoxal-5'-Phosphate |
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149 | (1) |
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Pyridoxal-5'-Phosphate-Stabilized Amino Acid Carbanions |
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149 | (2) |
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Mechanisms of Pyridoxal-5'-Phosphate-Dependent Reactions |
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151 | (7) |
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158 | (5) |
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Structures of Flavin Coenzymes |
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158 | (1) |
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Mechanisms of Flavin Catalysis |
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159 | (4) |
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163 | (2) |
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Structure and Role as a Carboxyl Carrier |
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163 | (1) |
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Chemistry of Biotin and N1-Carboxybiotin |
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164 | (1) |
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Mechanism of Biotin-Dependent Carboxylation |
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164 | (1) |
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Phosphopantetheine Coenzymes |
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165 | (2) |
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Structures of Phosphopantetheine Coenzymes |
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165 | (1) |
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Mechanism of Phosphopantetheine Action |
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165 | (2) |
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167 | (5) |
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Folate Compounds of One-Carbon Metabolism |
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168 | (2) |
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Enzymes in Tetrahydrofolate Metabolism |
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170 | (1) |
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Biological Importance of Folate |
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171 | (1) |
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Amino Acid--Based Coenzymes |
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172 | (17) |
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172 | (1) |
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Methylidene Imidazolinone--Dependent Deaminases |
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173 | (1) |
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174 | (15) |
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Coenzymes II: Metallic Coenzymes |
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189 | (64) |
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190 | (11) |
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Chemistry of B12 Coenzymes |
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190 | (3) |
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Adenosylcobalamin-Dependent Enzymes |
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193 | (6) |
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Methylcobalamin-Dependent Enzymes |
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199 | (2) |
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201 | (9) |
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Chemistry of Oxygen and Heme |
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201 | (3) |
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204 | (5) |
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Oxygen Binding and Electron Transfer |
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209 | (1) |
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210 | (7) |
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210 | (7) |
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217 | (1) |
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217 | (5) |
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218 | (1) |
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Reactions of Di-iron Enzymes |
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219 | (3) |
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222 | (5) |
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Molybdopterin and Tungstopterin |
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222 | (5) |
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227 | (7) |
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227 | (3) |
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230 | (4) |
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S-Adenosylmethionine and Iron-Sulfur Centers |
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234 | (3) |
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Catalytic Action of S-Adenosylmethionine and [ 4Fe--4S] Centers |
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234 | (2) |
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Stoichiometric Reactions of S-Adenosylmethionine and [ 4Fe--4S] Centers |
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236 | (1) |
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237 | (3) |
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Electrostatic Activation of Coordinated Water |
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237 | (1) |
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Electrostatic Activation of Enolization |
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238 | (2) |
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240 | (3) |
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240 | (1) |
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241 | (2) |
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243 | (4) |
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243 | (2) |
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245 | (2) |
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Long-Range Electron Transfer |
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247 | (6) |
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Biological Electron Transfer |
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247 | (1) |
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248 | (5) |
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253 | (44) |
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254 | (1) |
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254 | (1) |
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PALA and Aspartate Transcarbamylase |
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254 | (1) |
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255 | (13) |
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255 | (5) |
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β-Hydroxydecanoyl Thioester Dehydratase |
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260 | (2) |
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γ-Aminobutyrate Aminotransferase |
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262 | (6) |
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Kinetics of Slow-Binding and Tight-Binding Inhibition |
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268 | (2) |
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268 | (1) |
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269 | (1) |
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270 | (10) |
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271 | (3) |
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274 | (6) |
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280 | (17) |
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280 | (5) |
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285 | (4) |
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5-Enolpyruvoylshikimate-3-Phosphate Synthase |
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289 | (2) |
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291 | (6) |
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Acyl Group Transfer: Proteases and Esterases |
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297 | (36) |
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Chemistry of Acyl Transfer |
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297 | (3) |
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300 | (14) |
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301 | (10) |
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311 | (3) |
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314 | (3) |
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315 | (2) |
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317 | (1) |
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317 | (6) |
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318 | (2) |
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320 | (3) |
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323 | (5) |
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324 | (3) |
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327 | (1) |
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328 | (5) |
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328 | (1) |
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329 | (4) |
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333 | (54) |
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Aldose and Ketose Isomerases |
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333 | (8) |
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333 | (1) |
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334 | (1) |
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Triosephosphate Isomerase |
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335 | (6) |
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341 | (1) |
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341 | (5) |
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341 | (2) |
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343 | (1) |
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343 | (3) |
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346 | (18) |
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346 | (4) |
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350 | (2) |
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352 | (3) |
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UDP-Galactose 4-Epimerase |
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355 | (5) |
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360 | (1) |
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UDP-N-Acetylglucosamine-2-Epimerase |
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361 | (3) |
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364 | (2) |
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Δ5-3-Ketosteroid Isomerase |
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366 | (2) |
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368 | (11) |
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369 | (2) |
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371 | (5) |
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376 | (3) |
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379 | (8) |
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UDP-Galactopyranose Mutase |
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379 | (1) |
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379 | (8) |
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Decarboxylation and Carboxylation |
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387 | (46) |
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Chemistry of Decarboxylation and Carboxylation |
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387 | (1) |
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388 | (30) |
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389 | (5) |
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Amino Acid Decarboxylases |
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394 | (9) |
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Acetoacetate Decarboxylase |
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403 | (2) |
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Mevalonate Pyrophosphate Decarboxylase |
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405 | (2) |
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Radical-Based Decarboxylases |
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407 | (7) |
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Orotidine Monophosphate Decarboxylase |
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414 | (4) |
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418 | (15) |
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Ribulose-1,5-Bisphosphate Carboxylase |
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419 | (6) |
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Phosphoenolpyruvate Carboxylase |
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425 | (1) |
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Vitamin K--Dependent Carboxylase |
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426 | (7) |
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433 | (43) |
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α,β-Elimination/Addition Reactions |
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433 | (23) |
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Cofactor-Independent α,β-Elimination/Addition Reactions |
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434 | (6) |
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Cofactor-Dependent α,β-Elimination/Addition Reactions |
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440 | (16) |
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β,α-Elimination/Addition Reactions |
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456 | (6) |
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Methylidene Imidazolone--Dependent Elimination and Addition |
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456 | (6) |
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462 | (3) |
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Isomerization and Elimination |
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465 | (11) |
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465 | (1) |
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Coenzyme B12--Dependent Elimination |
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466 | (10) |
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Phosphotransfer and Nucleotidyltransfer |
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476 | (71) |
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Chemistry of Phosphoryl Group Transfer |
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476 | (11) |
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476 | (7) |
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483 | (1) |
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483 | (1) |
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Five-Member Ring Phosphoesters |
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484 | (3) |
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Enzymatic Phosphoryl Group Transfer |
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487 | (34) |
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Single and Double Displacements |
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487 | (2) |
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489 | (13) |
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Protein Phosphorylation: Protein Kinase A |
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502 | (7) |
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509 | (12) |
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Enzymatic Nucleotidyl Group Transfer |
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521 | (26) |
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521 | (18) |
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539 | (8) |
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ATP-Dependent Synthetases and Ligases |
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547 | (22) |
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Ligation and the Energy of ATP |
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547 | (1) |
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Activation by Phosphorylation |
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548 | (11) |
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548 | (6) |
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Carbamoyl Phosphate Synthetase |
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554 | (5) |
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Activation by Adenylylation |
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559 | (10) |
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559 | (2) |
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Aminoacyl-tRNA Synthetases |
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561 | (5) |
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566 | (3) |
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Glycosyl Group Transferases |
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569 | (28) |
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570 | (5) |
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Chemistry of Glycoside Hydrolysis |
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570 | (3) |
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Enzymatic Glycosyl Transfer |
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573 | (2) |
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575 | (12) |
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575 | (2) |
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577 | (7) |
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Purine Nucleoside Phosphorylase |
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584 | (3) |
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587 | (10) |
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587 | (2) |
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589 | (6) |
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595 | (2) |
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Nitrogen and Sulfur Transferases |
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597 | (20) |
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597 | (12) |
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Aspartate Aminotransferase |
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597 | (5) |
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602 | (2) |
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604 | (3) |
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Glutamine: PRPP Amidotransferase |
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607 | (2) |
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609 | (8) |
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611 | (1) |
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612 | (5) |
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Carbon-Carbon Condensation and Cleavage |
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617 | (38) |
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617 | (2) |
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Enolization of Acetyl CoA |
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619 | (11) |
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Acetyl CoA in Ester Condensations |
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619 | (1) |
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620 | (7) |
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627 | (3) |
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630 | (15) |
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631 | (3) |
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634 | (5) |
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Serine Hydroxymethyltransferase |
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639 | (6) |
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645 | (10) |
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Farnesyl Pyrophosphate Synthase |
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645 | (3) |
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648 | (7) |
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655 | (24) |
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655 | (2) |
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655 | (1) |
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656 | (1) |
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657 | (22) |
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Protein Farnesyltransferase |
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657 | (4) |
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Catechol O-Methyltransferase |
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661 | (4) |
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S-Adenosylmethionine Synthetase |
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665 | (5) |
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670 | (9) |
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679 | (31) |
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Pyridine Nucleotide--Dependent Dehydrogenases |
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680 | (14) |
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680 | (6) |
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686 | (1) |
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Short-Chain Alcohol Dehydrogenases |
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687 | (3) |
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Glyceraldehyde-3-P Dehydrogenase |
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690 | (3) |
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693 | (1) |
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Disulfide Oxidoreductases |
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694 | (4) |
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Dihydrolipoyl Dehydrogenase |
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694 | (4) |
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Ribonucleotide Reductases |
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698 | (12) |
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Classes of Ribonucleotide Reductases |
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700 | (5) |
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Structural Relationships of Ribonucleotide Reductases |
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705 | (5) |
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710 | (39) |
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710 | (12) |
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710 | (6) |
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716 | (2) |
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718 | (3) |
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721 | (1) |
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722 | (19) |
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722 | (1) |
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Cytochrome P450 Monooxygenases |
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722 | (5) |
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Iron-Methane Monooxygenase |
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727 | (5) |
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α-Ketoglutarate--Dependent Oxygenases |
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732 | (3) |
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735 | (2) |
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Copper-Methane Monooxygenase |
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737 | (1) |
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738 | (3) |
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741 | (8) |
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741 | (3) |
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744 | (5) |
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749 | (54) |
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750 | (7) |
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α-Ketoacid Dehydrogenase Complexes |
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750 | (1) |
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Pyruvate Dehydrogenase Complex |
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750 | (7) |
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757 | (6) |
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757 | (4) |
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761 | (2) |
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763 | (5) |
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|
763 | (4) |
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Nonribosomal Polypeptide Synthetases |
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767 | (1) |
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Ribosomal Protein Synthesis |
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768 | (9) |
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|
768 | (2) |
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770 | (7) |
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777 | (26) |
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|
777 | (5) |
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782 | (4) |
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|
786 | (6) |
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Myosin and Muscle Contraction |
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792 | (11) |
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803 | (6) |
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Appendix A: Haldane Relationships for Some Kinetic Mechanisms |
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|
803 | (1) |
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Appendix B: Inhibition Patterns for Three-Substrate Kinetic Mechanisms |
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|
804 | (1) |
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Appendix C: Equations for Number of Occupied Sites in the Binding of a Ligand to a Multisite Macromolecule |
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|
804 | (1) |
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Appendix D: Derivation of Steady-State Kinetic Equations by the King-Altman Method |
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|
805 | (4) |
Index |
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809 | |