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EC 4.2.1.168 Details
EC number
4.2.1.168
Accepted name
GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
Reaction
GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + NH3 (overall reaction);;(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] + 2-oxoglutarate + H2O;;(1b) 2-GDP-[(2S,3S,6R)-5-amino-6-methyl-3,6-dihydro-2H-pyran-3-ol] = 2-GDP-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] (spontaneous);;(1c) GDP-2-[(2S,3S,6R)-5-imino-6-methyloxan-3-ol] + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NH3 (spontaneous)
Other name(s)
colD (gene name)
Systematic name
GDP-4-dehydro-α-D-rhamnose 3-hydro-lyase
Comment
This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5′-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
History
created 2016
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EC Tree
1 Oxidoreductases
2 Transferases
3 Hydrolases
4 Lyases
4.1 Carbon-carbon lyases
4.2 Carbon-oxygen lyases
4.2.1 Hydro-lyases
4.2.1.1 carbonic anhydrase
4.2.1.2 fumarate hydratase
4.2.1.3 aconitate hydratase
4.2.1.4 citrate dehydratase
4.2.1.5 arabinonate dehydratase
4.2.1.6 galactonate dehydratase
4.2.1.7 altronate dehydratase
4.2.1.8 mannonate dehydratase
4.2.1.9 dihydroxy-acid dehydratase
4.2.1.10 3-dehydroquinate dehydratase
4.2.1.11 phosphopyruvate hydratase
4.2.1.12 phosphogluconate dehydratase
4.2.1.13 created 1961, deleted 2001
4.2.1.14 created 1961, deleted 2001
4.2.1.15 created 1961, deleted 1972
4.2.1.16 created 1961, deleted 2001
4.2.1.17 enoyl-CoA hydratase
4.2.1.18 methylglutaconyl-CoA hydratase
4.2.1.19 imidazoleglycerol-phosphate dehydratase
4.2.1.20 tryptophan synthase
4.2.1.21 created 1961, deleted 1964
4.2.1.22 cystathionine β-synthase
4.2.1.23 created 1961, deleted 1972
4.2.1.24 porphobilinogen synthase
4.2.1.25 L-arabinonate dehydratase
4.2.1.26 created 1965, deleted 2002
4.2.1.27 acetylenecarboxylate hydratase
4.2.1.28 propanediol dehydratase
4.2.1.29 created 1965, deleted 2004
4.2.1.30 glycerol dehydratase
4.2.1.31 maleate hydratase
4.2.1.32 L(+)-tartrate dehydratase
4.2.1.33 3-isopropylmalate dehydratase
4.2.1.34 (S)-2-methylmalate dehydratase
4.2.1.35 (R)-2-methylmalate dehydratase
4.2.1.36 homoaconitate hydratase
4.2.1.37 created 1972, deleted 1992
4.2.1.38 created 1972, deleted 2001
4.2.1.39 gluconate dehydratase
4.2.1.40 glucarate dehydratase
4.2.1.41 5-dehydro-4-deoxyglucarate dehydratase
4.2.1.42 galactarate dehydratase
4.2.1.43 2-dehydro-3-deoxy-L-arabinonate dehydratase
4.2.1.44 myo-inosose-2 dehydratase
4.2.1.45 CDP-glucose 4,6-dehydratase
4.2.1.46 dTDP-glucose 4,6-dehydratase
4.2.1.47 GDP-mannose 4,6-dehydratase
4.2.1.48 D-glutamate cyclase
4.2.1.49 urocanate hydratase
4.2.1.50 pyrazolylalanine synthase
4.2.1.51 prephenate dehydratase
4.2.1.52 dihydrodipicolinate synthase
4.2.1.53 oleate hydratase
4.2.1.54 lactoyl-CoA dehydratase
4.2.1.55 3-hydroxybutyryl-CoA dehydratase
4.2.1.56 itaconyl-CoA hydratase
4.2.1.57 isohexenylglutaconyl-CoA hydratase
4.2.1.58 crotonoyl-[acyl-carrier-protein] hydratase
4.2.1.59 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
4.2.1.60 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
4.2.1.61 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase
4.2.1.62 5α-hydroxysteroid dehydratase
4.2.1.63 created 1972, deleted 1978
4.2.1.64 created 1972, deleted 1978
4.2.1.65 3-cyanoalanine hydratase
4.2.1.66 cyanide hydratase
4.2.1.67 D-fuconate dehydratase
4.2.1.68 L-fuconate dehydratase
4.2.1.69 cyanamide hydratase
4.2.1.70 pseudouridylate synthase
4.2.1.71 created 1978, modified 1989, modified 2000, deleted 2004
4.2.1.72 created 1978, deleted 2000
4.2.1.73 protoaphin-aglucone dehydratase (cyclizing)
4.2.1.74 medium-chain-enoyl-CoA hydratase
4.2.1.75 uroporphyrinogen-III synthase
4.2.1.76 UDP-glucose 4,6-dehydratase
4.2.1.77 trans-L-3-hydroxyproline dehydratase
4.2.1.78 (S)-norcoclaurine synthase
4.2.1.79 2-methylcitrate dehydratase
4.2.1.80 2-oxopent-4-enoate hydratase
4.2.1.81 D(-)-tartrate dehydratase
4.2.1.82 xylonate dehydratase
4.2.1.83 4-oxalomesaconate hydratase
4.2.1.84 nitrile hydratase
4.2.1.85 dimethylmaleate hydratase
4.2.1.86 created 1989, deleted 2004
4.2.1.87 octopamine dehydratase
4.2.1.88 synephrine dehydratase
4.2.1.89 carnitine dehydratase
4.2.1.90 L-rhamnonate dehydratase
4.2.1.91 arogenate dehydratase
4.2.1.92 hydroperoxide dehydratase
4.2.1.93 ATP-dependent NAD(P)H-hydrate dehydratase
4.2.1.94 scytalone dehydratase
4.2.1.95 kievitone hydratase
4.2.1.96 4a-hydroxytetrahydrobiopterin dehydratase
4.2.1.97 phaseollidin hydratase
4.2.1.98 16α-hydroxyprogesterone dehydratase
4.2.1.99 2-methylisocitrate dehydratase
4.2.1.100 cyclohexa-1,5-dienecarbonyl-CoA hydratase
4.2.1.101 trans-feruloyl-CoA hydratase
4.2.1.102 created 2001, deleted 2001
4.2.1.103 cyclohexyl-isocyanide hydratase
4.2.1.104 cyanase
4.2.1.105 2-hydroxyisoflavanone dehydratase
4.2.1.106 bile-acid 7α-dehydratase
4.2.1.107 3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA hydratase
4.2.1.108 ectoine synthase
4.2.1.109 methylthioribulose 1-phosphate dehydratase
4.2.1.110 aldos-2-ulose dehydratase
4.2.1.111 1,5-anhydro-D-fructose dehydratase
4.2.1.112 acetylene hydratase
4.2.1.113 o-succinylbenzoate synthase
4.2.1.114 methanogen homoaconitase
4.2.1.115 UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting)
4.2.1.116 3-hydroxypropionyl-CoA dehydratase
4.2.1.117 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
4.2.1.118 3-dehydroshikimate dehydratase
4.2.1.119 enoyl-CoA hydratase 2
4.2.1.120 4-hydroxybutanoyl-CoA dehydratase
4.2.1.121 colneleate synthase
4.2.1.122 tryptophan synthase (indole-salvaging)
4.2.1.123 tetrahymanol synthase
4.2.1.124 arabidiol synthase
4.2.1.125 dammarenediol II synthase
4.2.1.126 N-acetylmuramic acid 6-phosphate etherase
4.2.1.127 linalool dehydratase
4.2.1.128 lupan-3β,20-diol synthase
4.2.1.129 squalene—hopanol cyclase
4.2.1.130 D-lactate dehydratase
4.2.1.131 carotenoid 1,2-hydratase
4.2.1.132 2-hydroxyhexa-2,4-dienoate hydratase
4.2.1.133 copal-8-ol diphosphate hydratase
4.2.1.134 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
4.2.1.135 UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining)
4.2.1.136 ADP-dependent NAD(P)H-hydrate dehydratase
4.2.1.137 sporulenol synthase
4.2.1.138 (+)-caryolan-1-ol synthase
4.2.1.139 pterocarpan synthase
4.2.1.140 gluconate/galactonate dehydratase
4.2.1.141 2-dehydro-3-deoxy-D-arabinonate dehydratase
4.2.1.142 5′-oxoaverantin cyclase
4.2.1.143 versicolorin B synthase
4.2.1.144 3-amino-5-hydroxybenzoate synthase
4.2.1.145 capreomycidine synthase
4.2.1.146 L-galactonate dehydratase
4.2.1.147 5,6,7,8-tetrahydromethanopterin hydro-lyase
4.2.1.148 2-methylfumaryl-CoA hydratase
4.2.1.149 crotonobetainyl-CoA hydratase
4.2.1.150 short-chain-enoyl-CoA hydratase
4.2.1.151 chorismate dehydratase
4.2.1.152 hydroperoxy icosatetraenoate dehydratase
4.2.1.153 3-methylfumaryl-CoA hydratase
4.2.1.154 tetracenomycin F2 cyclase
4.2.1.155 (methylthio)acryloyl-CoA hydratase
4.2.1.156 L-talarate dehydratase
4.2.1.157 (R)-2-hydroxyisocaproyl-CoA dehydratase
4.2.1.158 galactarate dehydratase (D-threo-forming)
4.2.1.159 dTDP-4-dehydro-6-deoxy-α-D-glucopyranose 2,3-dehydratase
4.2.1.160 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one isomerase/dehydratase
4.2.1.161 bisanhydrobacterioruberin hydratase
4.2.1.162 6-deoxy-6-sulfo-D-gluconate dehydratase
4.2.1.163 2-oxo-hept-4-ene-1,7-dioate hydratase
4.2.1.164 dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase
4.2.1.165 chlorophyllide a 31-hydratase
4.2.1.166 phosphinomethylmalate isomerase
4.2.1.167 (R)-2-hydroxyglutaryl-CoA dehydratase
4.2.1.168 GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
4.2.1.169 3-vinyl bacteriochlorophyllide d 31-hydratase
4.2.1.170 2-(ω-methylthio)alkylmalate dehydratase
4.2.1.171 cis-L-3-hydroxyproline dehydratase
4.2.1.172 trans-4-hydroxy-L-proline dehydratase
4.2.1.173 ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase
4.2.1.174 peregrinol diphosphate synthase
4.2.1.175 (R)-3-(aryl)lactoyl-CoA dehydratase
4.2.1.176 L-lyxonate dehydratase
4.2.1.177 (2S)-3-sulfopropanediol dehydratase
4.2.1.178 difructose-dianhydride-III synthase
4.2.1.179 difructose-anhydride-I synthase
4.2.1.180 (E)-benzylidenesuccinyl-CoA hydratase
4.2.2 Acting on polysaccharides
4.2.3 Acting on phosphates
4.2.99 Other carbon-oxygen lyases
4.3 Carbon-nitrogen lyases
4.4 Carbon-sulfur lyases
4.5 Carbon-halide lyases
4.6 Phosphorus-oxygen lyases
4.7 carbon-phosphorus lyases
4.8 Nitrogen-oxygen lyases
4.98 ATP-independent chelatases
4.99 Other lyases
5 Isomerases
6 Ligases
7 Translocases
7.1 Catalysing the translocation of hydrons
7.2 Catalysing the translocation of inorganic cations
7.3 Catalysing the translocation of inorganic anions and their chelates
7.4 Catalysing the translocation of amino acids and peptides
7.5 Catalysing the translocation of carbohydrates and their derivatives
7.6 Catalysing the translocation of other compounds