SUBJECT INDEX accABCD genes, in flavanone synthesis, 177 Aclacinomycin A, 96 Acceptors, of DesVII–Des VIII, 68 biosynthetic pathway of, 100 Acceptor specificity, in directed molecular structure of, 95 glycosyltransferase evolution, 106 Aclarubicins, 96 Acetaldehyde, in ethanol production, molecular structure of, 95 191–192 Acridone synthase (ACS), in polyketide Acetaphenone, in flavonoid synthesis, 176 synthesis, 169 Acetate kinase (ACK), in malonyl-CoA Actinomycetes, macrolide antibiotics from, 64 formation, 179, 180 Activation, of inosine 50-monophosphate Acetic acid, in combinatorial pathway design, dehydrogenase, 36–39 129 Acute myelogenous leukemia, enediynes Acetoacetyl-CoA (coenzyme A) versus, 89 in ethanol production, 192 Acyclic carotenoids, synthesis of, 165 in MVA pathway, 153, 154 Acyclic xanthophylls, biosynthesis of, 124 Acetoacetyl-CoA ligase, in MVA pathway, Acyl carrier protein (ACP) 154 in combinatorial pathway design, 129 Acetoacetyl-CoA thiolase, in MVA pathway, protein–protein interactions and, 133–134 153 Acyltransferase (AT) domain Acetyl-CoA in combinatorial pathway design, 129, in butanol production, 196 130, 132 in ethanol production, 192 protein–protein interactions and, 133 in MVA pathway, 153, 154 Adenosine monophosphate (AMP), polyketides and, 167 biosynthesis of, 2, 3 Acetyl-CoA carboxylase (ACC) Adriamycin, 95–96, 98 in flavanone synthesis, 177–179, 180 molecular structure of, 95 in malonyl-CoA formation, 179 Aerobacter aerogenes, IMPDH in, 5, 18, 26 Acetyl-CoA synthase (ACS), in malonyl-CoA Aglycones. See also Aglycons formation, 179 anthracyclines and, 98–101 N-Acetyl-glucosamine, in teicoplanin, 83 calicheamicin, 91, 92 Acetyl phosphate, in malonyl-CoA macrolide glycosyltransferases and, 66 formation, 179 of vicenistatin, 93 3-Acetylpyridine adenine dinucleotide Aglycone substrates, accepted by OleD, 74 (APAD), in Tritrichomonas foetus,21 Aglycon exchange reactions AcinetobacterCOPYRIGHTED bayli ADP1, in wax ester CalG1-catalyzed, MATERIAL 92 biosynthesis, 124–125 CalG4-catalyzed, 93 Advances in Enzymology and Related Areas of Molecular Biology, Volume 76 Edited by Eric J.Toone Copyright ° 2009 by John Wiley & Sons, Inc. 243 244 SUBJECT INDEX Aglycon exchanges, erythromycins shikimates and, 173–174 and, 70 Amino acid sequences, in glycosyltransferase Aglycons. See also Aglycones design, 101–103 anthracyclines and, 98–101 Aminocoumarins, 86–88 avermectin and, 76–77 molecular structures of, 87 in natural product glycosylation, 59 Aminomalonyl-ACP extender unit, in oleandomycin and, 74–75 combinatorial pathway design, 129, 130 in vicenistatin reactions, 94–95 Ammonia, in purine nucleotide biosynthesis, 2 Aglycon specificity, methymycin and, Ammonia-limited conditions, biosynthesis 66–69 optimization under, 141–142 Agrobacterium tumefaciens Amorpha-4,11-diene monooxygenase, in in artemisinin production, 158 MVA pathway, 154 in ubiquinone production, 166–167 Amorphadiene Aklavinone biosynthetic pathway, 72 in artemisinin synthesis, 158 AknK glycosyltransferase, 96 in terpene biosynthesis, 138 mechanism of action of, 99 Amorphadiene synthase reactions catalyzed by, 97 in artemisinin synthesis, 158 AknS glycosyltransferase, 96, 98, in MVA pathway, 154 100–101 AmpD1 glycosyltransferase, calicheamicin mechanism of action of, 99 and, 93 aknT gene, 98 AMP-dependent protein kinase (ADPK), 41 AknT glycosyltransferase, 98, 100–101 Angiogenesis, flavonols in, 182 mechanism of action of, 99 D6,7-Anhydroerythromycin C, synthesis of, Alanine 172 cytochrome-P450 enzymes and, 189 Anomeric kinases, in natural product in hydroxylated flavonoid synthesis, 190 glycosylation, 59 protein dynamics and, 34 Anthocyanidin synthase (ANS) Alcohol dehydrogenase (Ec-adhE), in butanol in anthocyanin synthesis, 184–185 production, 196–197 in flavonoid pathway, 178–179 Alcohol dehydrogenase (adh), in ethanol Anthocyanins, 175–176, 183–185 production, 192 medicinal uses of, 183 Aldehydes, in epothilone synthesis, 169 from plant cell cultures, 155 Alkaloids, in combinatorial pathway design, synthesis of, 178–179 128 Anthracyclines, 95–101 a-carotene, in carotenoid biosynthesis, 161, mechanism of action of, 96–101 162 Anthurium andraeanum, in anthocyanin a-helix synthesis, 184 of glycosyltransferases, 61, 62 Antibiotics of IMPDH, 33–34 aminocoumarins as, 86–88 a-zearalenol, 94 aromatic polyketides as, 95–101 Amino acid residues, in polyketide synthesis, enediynes as, 88–93 169 glycopeptides as, 78–86 Amino acids macrolactams as, 93–95 in flavanone synthesis, 177 macrolides as, 64–78 in glycosyltransferase classification, 60 nonribosomal peptides as, 78–86 in purine nucleotide biosynthesis, 2 polyketides as, 167 SUBJECT INDEX 245 Anticancer agents/drugs artemisinin from, 157 anthracyclines as, 96 in terpene biosynthesis, 138 terpenoids as, 152 Artemisinic acid pathway, 154 Antimicrobial agents, terpenoids as, 152 Artemisinin, 134, 154 Antioxidants, ubiquinone, 166–167 enhanced production of, 157–158 Apiferol, in flavonoid pathway, 178–179 microbial synthesis of, 158 Apples from plant cell cultures, 157–158 in anthocyanin synthesis, 184 synthesis of, 157 flavonols from, 182–183 in terpene biosynthesis, 138 appY gene, in carotenoid biosynthesis, 164 yeast synthesis of, 158–159 Aquifex aelicus, peptidoglycan GTs of, 62 Aryltetrasaccharide, in calicheamicin, 89 araBAD promoter, carotenoid biosynthesis Aspartate, vancomycin Gtf’s and, 62 and, 140 Aspartate–alanine substitutions, in IMPDH, Arabidopsis thaliana 24–25 in anthocyanin synthesis, 185 Astaxanthin flavonols from, 182–183 biosynthesis of, 164 resveratrol from, 186 in carotenoid biosynthesis, 162 Arabinose, oleandomycin and, 75 ATP binding, to IMPDH subdomain, 41 araGT gene, 101 Autosomal dominant retinitis pigmentosa AraGT glycosyltransferase, 101 (adRP), 40, 41 Aranciamycin, rhamnosylation of, 101 aveBI gene, 75 ArcA regulon, in ethanol production, 193 AveBI glycosyltransferase, 75–77 Archaea calicheamicin and, 93 IMPDH from, 5, 11 reactions catalyzed by, 76 in KEGG database, 126 Avermectin, 75–77 Arginine molecular structure of, 57, 76 IMPDH ligand binding and, 299 reactions of, 76 protein dynamics and, 34–35 AviGT4 glycosyltransferase, 61 species-selective affinity and, 35 Avilamycin, AviGT4 glycosyltransferase of, Aristolocolchine, optimizing biosynthetic 61 pathway for, 139 Azepinomycin, as IMPDH inhibitor, 16 AroE catalysis, in shikimate synthesis, 174, Azithromycin, 64 175 molecular structure of, 65 aro enzymes, in shikimate synthesis, 174–175 Aromatic amino acids, shikimates and, Baccatin III, in Taxol synthesis, 159 173–174 Bacillus subtilis, MEP pathway in, 153 Aromatic flavonoid derivatives, 173–190 Bacteria. See also Microbial synthesis from cytochrome-P450, 186–190 as biofuel synthesis biocatalysts, 191 flavonoids, 175–185 in butanol production, 196 shikimates, 173–175 carotenoid biosynthesis in, 161–165 stilbenes, 185–186 carotenoids in, 160 Aromatic polyketides, 95–101 enterobactins from, 83–85 Artemisia annua in ethanol production, 191–192 artemisinin from, 157, 158, 159 IMPDH from, 5–8, 11 in terpene biosynthesis, 138 in KEGG database, 126 Artemisinic acid, 154 MEP pathway in, 153–155 246 SUBJECT INDEX Bacteria. (Continued) b-zearalenol, 94 terpene cyclases from, 137, 138 Binding sites, of inosine 50-monophosphate ubiquinone from, 166–167 dehydrogenase, 26–29 unnatural carotenoids from, 165–166 Biocatalysis database, 127–128 vancomycin-resistant, 79 Biocatalyst-based processes, green chemistry Bacteriophage P1, in shikimate synthesis, 175 and, 152 Bacteriophage T5, in astaxanthin synthesis, Biocatalysts, microorganisms as, 191 165 BioCyc database, 127 Bacteriophage T7 Biodegradation database, 127–128 in flavanone synthesis, 177 Biofuels, 191–197 in Taxol synthesis, 160 butanol, 191, 195–197 Baker’s yeast, in carotenoid biosynthesis, 163 ethanol, 191–195 Barrel fold structure microbial synthesis of, 152 in IMPDH ligand binding, 27 utility of, 191 in IMPDH molecules, 9 Bioinformatics Bateman domains green chemistry and, 152 defined, 40 in polyketide synthesis, 168–169 of inosine 50-monophosphate in protein engineering and pathway dehydrogenase, 37, 39–42 design, 123 in various proteins, 41–42 Bioreactors, in flavonoid bioproduction, Benzalacetone, medicinal applications of, 168 175 Benzalacetone synthase (BAS), in polyketide Biosynthesis, 151–217 synthesis, 169 of anthocyanins, 184 Benzaldehyde, in flavonoid synthesis, 176 of aromatic derivatives, 173–190 Benzimidazole NAD analog (BAD), 16 of biofuels, 191–197 Berberine, from plant cell cultures, 155 of carotenoids, 160–167 b-carotene of cell walls, 62 in astaxanthin biosynthesis, 164, 165 of epothilones, 169, 170–171 in carotenoid biosynthesis, 161, 162 of ethanol, 191–195 b-carotene hydroxylase (crtZ) future of, 142–143 in astaxanthin biosynthesis, 164 of guanine, 14 in carotenoid biosynthesis, 162 of isoflavones, 180–181 b-carotene ketolase (crtW) of natural products, 197–198 in astaxanthin biosynthesis, 164 of polyketides, 167–173 in carotenoid biosynthesis, 162 of purine nucleotides, 1–4 b-estradiol, 94 of terpenoids, 152–160 b-methylene-biphosphonate (b-TAD, Biosynthetic enzymes b-CH2-TAD). See also Tiazofurin in natural product glycosylation, 59 adenine dinucleotide (TAD) searching for, 124 in IMPDH activation, 38 Biosynthetic pathways IMPDH crystal structure and, 8, 11, 12 design of, 128–138 in IMPDH ligand binding, 28 diversification of, 128–138 kinetic properties of, 5, 6 optimization of, 128, 137, 138–142 NAD analogs of IMPDH and, 16 Biosynthetic reaction sequences, combina- species-selective affinity