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Enzymatic Redox Chemistry 149 NADH NAD + flavoprotein reductase FAD FADH 2 R + O 2 ferredoxin dioxygenase [FeS] red Fe 2+ [FeS] ox HO OH R Figure 6.39 Electron transfer in dihydroxylating dioxygenases. dihydroxylating dioxygenases. Both these classes of enzyme are involved in the bacterial degradation of aromatic compounds in the environment. As shown in Figure 6.38, the dihydroxylating dioxygenases catalyse the oxidative conversion of an aromatic substrate into the corresponding cis-dihydrodiol. The cis-diol is then oxidised by a class of NAD þ -dependent dehydrogenases into the corresponding aromatic diol, or catechol. Oxidative cleavage of the aromatic ring is then carried out in one of two ways. Cleavage of the carbon–carbon bond between the two hydroxyl groups and insertion of both atoms of dioxygen is catalysed by non-haem iron(III)-dependent intradiol dioxygenases. Alternatively, cleavage of a carbon–carbon bond adjacent to the two hydroxyl groups and insertion of two oxygen atoms can be catalysed by non-haem iron(II)- dependent extradiol dioxygenases. The dihydroxylating dioxygenases are multi-component enzymes whose sub-units are involved in electron transfer. Two electrons are transferred by a Xavoprotein reductase sub-unit from NADH to FADH 2 . The two electrons are then transferred singly to iron–sulphur clusters contained in a ferredoxin subunit. These electrons are then transferred to the active site of the dioxygenase sub-unit, as shown in Figure 6.39. The mechanisms of these non-haem iron-dependent dioxygenases are not well understood, but all presumably involve activation of dioxygen by electron transfer from the iron cofactor. In the case of the dihydroxylating dioxygenases, formation of a four-membered dioxetane intermediate has been proposed, followed by reduction to generate the cis-diol product, as shown in Figure 6.40. This mechanism would explain the cis-stereochemistry of the product and the incorporation of 18 O into both hydroxyl groups from 18 O 2 . However, the formation of dioxetane intermediates from ground state oxygen is endothermic and therefore apparently unlikely.
150 Chapter 6 R R R O 2 , Fe 2+ O O [2H] OH OH Figure 6.40 Dioxetane mechanism for dihydroxylating dioxygenases. O O − O− O Fe n+ − O O − O Fe n+ O acyl migration Fe 2+ alkenyl migration Fe 3+ Figure 6.41 Possible mechanisms for catechol dioxygenases. O O O O O O − OH Fe II − OH Fe III H O O O − OH extradiol O − O O O − intradiol Figure 6.42 Active site of protocatechuate 4,5-dioxygenase (PDB Wle 1B4U), showing the tridentate His, His, Glu motif responsible for binding the non-haem iron(II) cofactor. This motif is found in many non-haem iron-dependent oxygenases. The bound substrate is shown in black. Picture prepared using RASMOL.
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Introduction to Enzyme and Coenzyme
Page 4 and 5:
Introduction to Enzyme and Coenzyme
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Contents Preface Representation of
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Contents vii 8 Enzymatic Addition/E
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Representation of Protein Three-Dim
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2 Chapter 1 H 2 N O NH 2 + H 2 O Ja
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4 Chapter 1 Table 1.1 The vitamins.
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6 Chapter 1 has very diVerent biolo
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2 All Enzymes are Proteins 2.1 Intr
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10 Chapter 2 (Gln). There are three
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12 Chapter 2 AAA Lys ACA Thr AGA Ar
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14 Chapter 2 H N O H N O Figure 2.8
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16 Chapter 2 (a) (b) Figure 2.12 St
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18 Chapter 2 Figure 2.14 Structure
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20 Chapter 2 (a) X Y Enzyme + Subst
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22 Chapter 2 maintaining protein te
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24 Chapter 2 surface glycoprotein g
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26 Chapter 2 O-linked glycosylation
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28 Chapter 2 Metalloproteins I. Ber
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30 Chapter 3 O N H R CO 2 H acylase
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32 Chapter 3 (a) Free energy uncata
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34 Chapter 3 Ester k rel Effective
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36 Chapter 3 3.4 The importance of
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38 Chapter 3 pKa Tyrosine CH 2 O H
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40 Chapter 3 glycoside hydrolysis (
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42 Chapter 3 O O Glu 143 O − R H
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44 Chapter 3 the hydroxyl groups of
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46 Chapter 3 E + S E + S ES' ES ‘
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48 Chapter 3 Examination of protein
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50 Chapter 3 (Note: Similar results
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52 Chapter 4 (1) Direct UV (2) Radi
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54 Chapter 4 Figure 4.3 PuriWcation
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56 Chapter 4 The two kinetic consta
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58 Chapter 4 Lineweaver−Burk Plot
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60 Chapter 4 E + S K i EI+ I ES E +
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62 Chapter 4 (2) by treatment with
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64 Chapter 4 In general the stereoc
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H D T CO 2 H CO − 2 T HO D H −
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68 Chapter 4 4.5 The existence of i
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70 Chapter 4 18O 18O 18 O O P O −
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72 Chapter 4 If a reaction involves
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74 Chapter 4 O D H ketosteroid isom
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76 Chapter 4 Table 4.3 Group speciW
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78 Chapter 4 [S] (mM) Rate of produ
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80 Chapter 4 Enzyme kinetics I.H. S
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82 Chapter 5 O = C NHR peptidase H
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84 Chapter 5 non-speciWc protease c
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86 Chapter 5 His 57 His 57 Asp 102
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88 Chapter 5 Other serine proteases
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90 Chapter 5 Figure 5.8 Structure o
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92 Chapter 5 now predominate Perhap
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OH R O Zn 2+ O O O Ph Glu 270 H 2 N
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96 Chapter 5 CASE STUDY: HIV-1 prot
Page 109 and 110: 98 Chapter 5 HO Transition state pe
Page 111 and 112: 100 Chapter 5 The aminoacyl group o
Page 113 and 114: 102 Chapter 5 5.5 Enzymatic phospho
Page 115 and 116: 104 Chapter 5 Figure 5.29 Structure
Page 119 and 120: 108 Chapter 5 Adenosine 5 0 -tripho
Page 121 and 122: 110 Chapter 5 functional group. Gly
Page 123 and 124: 112 Chapter 5 CH 2 OH O RO HO OH O
Page 125 and 126: 114 Chapter 5 to these atoms that t
Page 127 and 128: 116 Chapter 5 Problems (1) Using pa
Page 129 and 130: 118 Chapter 5 (6) Retaining glycosi
Page 131 and 132: 120 Chapter 5 J.R. Knowles (1980) E
Page 133 and 134: 122 Chapter 6 +1.0 Redox potential
Page 135 and 136: Table 6.1 Classes of redox enzymes.
Page 137 and 138: 126 Chapter 6 An important point is
Page 139 and 140: 128 Chapter 6 O H − OH − O OH H
Page 141 and 142: 130 Chapter 6 one-electron transfer
Page 143 and 144: 132 Chapter 6 (a) R N H + N O R N H
Page 145 and 146: 134 Chapter 6 Inactivation by trany
Page 149 and 150: 138 Chapter 6 (a) (b) Figure 6.23 S
Page 151 and 152: 140 Chapter 6 glutathione called tr
Page 153 and 154: 142 Chapter 6 neither has a stable
Page 155 and 156: 144 Chapter 6 of the haem cofactor
Page 157 and 158: 146 Chapter 6 Figure 6.33 Active si
Page 159: 148 Chapter 6 HO H N N O O H N prol
Page 163 and 164: 152 Chapter 6 CoA. Explain these re
Page 165 and 166: 154 Chapter 6 NADH models O. Almars
Page 167 and 168: 7 Enzymatic Carbon-Carbon Bond Form
Page 169 and 170: 158 Chapter 7 O H − OH O − O H
Page 173 and 174: 162 Chapter 7 Figure 7.6 Active sit
Page 175 and 176: 164 Chapter 7 7.3 Claisen enzymes I
Page 177 and 178: 166 Chapter 7 CoAS O EnzB − H D T
Page 179 and 180: 168 Chapter 7 onto the acetyl-thioe
Page 181 and 182: 170 Chapter 7 In the case of erythr
Page 183 and 184: 172 Chapter 7 O HO O − O ATP ADP
Page 185 and 186: 174 Chapter 7 CO 2 − vitamin K-de
Page 187 and 188: 176 Chapter 7 7.8 Thiamine pyrophos
Page 189 and 190: 178 Chapter 7 HN N + N H NH S O OPP
Page 191 and 192: 180 Chapter 7 O OH OH camphor geran
Page 193 and 194: 182 Chapter 7 CH 3 * OPP (−)pinen
Page 197 and 198: 186 Chapter 7 C C C C C O OCH 3 C H
Page 199 and 200: 188 Chapter 7 AcO HO HO NHAc O OH +
Page 201 and 202: 190 Chapter 7 (9) Usnic acid is a n
Page 203 and 204: 192 Chapter 7 Radical couplings W.M
Page 205 and 206: 194 Chapter 8 C-O cleavage H E1 H C
Page 207 and 208: 196 Chapter 8 leads to the formatio
Page 209 and 210: 198 Chapter 8 aconitase citrate cis
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200 Chapter 8 *H R H H CO 2 − NH
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202 Chapter 8 EnzB − 2 H − O 2
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204 Chapter 8 involves no change in
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206 Chapter 8 Glyphosate H H N CO
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208 Chapter 8 (5) Chorismic acid (s
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9 Enzymatic Transformations of Amin
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CO − − 2 CO 2 H H CO 2 − N +
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214 Chapter 9 - BEnz CO − 2 Cl H
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216 Chapter 9 Arg 292 Arg 292 Lys 2
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218 Chapter 9 Arg 292 Asp 292 HN H
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220 Chapter 9 S − B 1 Enz H − C
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222 Chapter 9 9.6 N-Pyruvoyl-depend
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224 Chapter 9 The biosyntheses of n
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226 Chapter 9 Further reading Gener
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228 Chapter 10 B 1 - H + NH 3 CO
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230 Chapter 10 ‘low-barrier’ +
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232 Chapter 10 H S C 6 H 13 HN His
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234 Chapter 10 O H NH 3 CO 2 − CO
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236 Chapter 10 sub-units. Each sub-
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238 Chapter 10 Further reading Gene
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11 Radicals in Enzyme Catalysis 11.
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242 Chapter 11 CH 2 Co III Ad H OH
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244 Chapter 11 − O 2 C − O CO
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246 Chapter 11 H N H O 734 H N H PF
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248 Chapter 11 H H* + H + H 3 N CO
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250 Chapter 11 O HN NH + H 3 N H 3
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252 Chapter 11 cofactor is involved
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254 Chapter 11 Protein Radicals J.
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256 Chapter 12 self-splicing reacti
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258 Chapter 12 Figure 12.2 Structur
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260 Chapter 12 antigen combining si
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262 Chapter 12 R O OR' OH − R O
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264 Chapter 12 CO 2 − − O 2 C O
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266 Chapter 12 (1) Selective substr
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268 Chapter 12 HO O HO OH HO OH O O
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270 Chapter 12 Problems (1) How rev
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Appendix 1: Cahn-Ingold-Prelog Rule
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Appendix 2: Amino Acid Abbreviation
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276 Appendix 3 Preparation of orang
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278 Appendix 4 (2) Intramolecular a
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280 Appendix 4 from water at a-posi
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282 Appendix 4 Chapter 8 (1) Treat
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284 Appendix 4 (b) Formation of rad
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286 Index b-hydroxydecanoyl thioest
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288 Index glycosylation 26-7 glysop
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290 Index phenylalanine ammonia lya
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292 Index transition states 31-2 an
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