Appendix 1: Enzymatic reactions by metabolic pathway and EC number

The EC (European Commission) number is a classification system for enzymes, organized by the type of reaction catalyzed. You can use the list below to search this textbook for information about the reaction catalyzed by a given enzyme. You can also use the EC numbers to search for information in databases such as SwissProt Enzyme Nomenclature Database (http://enzyme.expasy.org) or the BRENDA Comprehensive Enzyme Information System (http://www.brenda-enzymes.org).

Glycolysis

Hexose kinase (EC 2.7.1.1)

Phosphoglucose isomerase (EC 5.3.1.9)

Phosphofructokinase (EC 2.7.1.56)

Fructose 1,6-bisphosphate aldolase (EC 4.1.2.13)

Triose phosphate isomerase (5.3.1.1)

Gyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12)

Phosphoglycerate kinase (EC 2.7.2.3)

Phosphoglycerate mutase (EC 5.4.2.1)

Enolase (EC 4.2.1.11)

Pyruvate kinase (EC 2.7.1.40)

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14)

Gluconeogenesis

Pyruvate carboxylase (EC 6.4.1.1)

Phosphoenolpyruvate carboxykinase (EC 4.1.1.32)

Phosphoglycerate kinase (EC 2.7.2.3)

Fructose 1,6-bisphosphatase (EC 3.1.3.11)

Glucose 6-phosphatase (EC 3.1.3.9)


Citric Acid (TCA) Cycle

Pyruvate dehydrogenase complex (EC 1.2.4.1)

Citrate synthase (EC 2.3.3.8)

Aconitase (EC 4.2.1.3)

Isocitrate dehydrogenase (EC 1.1.1.42)

α-ketoglutarate dehydrogenase complex:

Oxoglutarate dehydrogenase (EC 1.2.4.2)

Dihydrolipoyl succinyltransferase (EC 2.3.1.61)

Dihydrolipoyl dehydrogenase (EC 1.8.1.4)

Succinyl CoA synthetase (EC 6.2.1.4)

Succinate dehydrogenase (EC 1.3.5.1)

Fumarase (EC 4.2.1.2)

Malate dehydrogenase (EC 1.1.1.37)

Fermentation

Pyruvate decarboxylase (EC 4.1.1.1)

Alcohol dehydrogenase (EC 1.1.1.1)

Lactate dehydrogenase ((EC 1.1.1.27)

Pentose phosphate pathway/Calvin Cycle

Glucose 6-phosphate dehydrogenase (EC 1.1.1.49)

Gluconolactonase (EC 3.1.1.17)

6-Phosphogluconate dehydrogenase (EC 1.1.1.43)

Phosphopentose epimerase (EC 5.1.3.1)

Phosphopentose isomerase (EC 5.3.1.6)

Transketolase (EC 2.2.1.1)

Transaldolase (EC 2.2.1.2)

Rubisco (EC 4.1.1.39)

Aldolase (EC 4.1.2.13)

Fatty acid oxidation

Acyl CoA synthetase (EC 6.2.1.1)

Carnitine acyltransferase (EC 2.3.1.21)

Acyl CoA dehydrogenase (eg. EC 1.3.99.13)

Enoyl CoA hydratase (eg. 4.2.1.74)

3-hydroxyacyl CoA dehydrogenase (EC 1.1.1.35)

β-Keto thiolase (EC 2.3.1.16)

Unsaturated fatty acids:***

cis-Enoyl-CoA isomerase (eg. EC 5.3.3.8)

2,4-Dienoyl CoA reductase (EC 1.3.1.34)

Glycerol phosphate dehydrogenase (EC 1.1.1.8)

Fatty acid biosynthesis

Acetyl CoA carboxylase (EC 6.4.1.2)

Acyl CoA synthetase (EC 6.2.1.1)

ACP transacylase (EC 2.3.1.38)

β-ketoacyl-ACP synthase (EC 2.3.1.41)

β-ketoacyl-ACP hydrogenase (EC 1.1.1.35)

3-hydroxyacyl dehydratase (EC 4.2.1.58)

Enoyl-ACP reductase (EC 1.3.1.10)

Acyl-CoA dehydrogenase (EC 1.3.99.3)

Monoacylglycerol acyltransferase (EC 2.3.1.22)

Isoprenoid biosynthesis

Mevalonate pathway (from acetyl CoA):

Acetoacetyl CoA acetyltransferase (EC 2.3.1.9)

3-hydroxy-3-methylglutaryl-CoA synthase (EC 2.3.3.10)

HMG-CoA reductase (EC 1.1.1.34)

Mevalonate kinase (EC 2.7.1.36)

Phosphomevalonate kinase (EC 2.7.4.2)

Mevalonate diphosphate decarboxylase (EC 4.1.1.33)

Deoxyxylulose pathway (from pyruvate and glyceraldehyde phosphate):

Deoxyxylulose phosphate synthase (EC 2.2.1.7)

Deoxyxylulose phosphate reductoisomerase (EC 1.1.1.267

MEP cytidylyltransferase (EC 2.7.7.60)

CDP-ME kinase (EC 2.7.1.148)

Methylerithritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12)

other:***

isopentenyl diphosphate isomerase (EC 5.3.3.2)

geranyl diphosphate synthase (EC 2.5.1.1)

farnesyl diphosphate synthase (EC 2.5.1.10)

squalene synthase (EC 2.5.1.21)

oxidosqualene cyclase (EC 5.4.99.7)

DMAPP-tryptophan synthase (EC 2.5.1.34)

Deoxyribonucleotide biosynthesis

PRPP synthetase (EC 2.7.6.1)

UMP (from ammonia, bicarbonate, and aspartate):

Carbamoyl phosphate synthase (EC 6.3.5.5)

Aspartate carbamoyltransferase (EC 2.1.3.2)

Dihydroorotase (EC 2.5.2.3) 4

Dihydroorotate dehydrogenase (EC 1.3.3.1)

Orotate phosphoribosyltransferase (EC 2.4.2.10)

Orotidine monophosphate decarboxylase (EC 4.1.1.23)

TMP (from dUMP):

Thymidylate synthase (EC 2.1.1.45)

CTP: (from UTP):

CTP synthase (EC 6.3.4.2)

IMP (from PRPP):

Glutamine phosphoribosyl amidotransferase (EC 2.4.2.14)

Glycinamide ribonucleotide synthetase (EC 6.3.4.13)

GAR transformylase (EC 2.1.2.2)

FGAM synthetase (EC 6.3.5.3)

Aminoimidazole ribonucleotide synthetase (EC 6.3.3.1)

Aminoimidazole ribonucleotide carboxylase (EC 4.2.1.1)

SAICAR synthetase (EC 6.3.2.6)

Adenylosuccinate lyase (EC 4.3.2.2)

AICAR transformylase (EC 2.1.2.3)

IMP cyclohydrolase (EC 3.5.4.10)

AMP (from IMP):

Adenylosuccinate synthetase (EC 6.3.4.4)

Adenylosuccinate lyase (EC 4.3.2.2)

GMP (from IMP):

IMP dehydrogenase (EC 1.1.1.205)

GMP synthetase (EC 6.3.5.2)

Deoxyribonucleotides:

Ribonucleotide reductase (EC 1.17.4.1)

Nucleotide degradation

Cytidine (to uridine):

Cytidine deaminase (EC 3.5.4.5)

Uridine (to malonyl CoA):

Uridine phosphorylase (EC 2.4.2.3)

Dihydropyrimidine dehydrogenase (EC 1.3.1.2)

Dihydropyrimidase (EC 3.5.2.2)

β-ureidopropionase (EC 3.5.1.6)

Thymidine (to succinyl CoA):

Thymidine phosphorylase (EC 2.4.2.4)

Dihydropyrimidine dehydrogenase (EC 1.3.1.2)

Dihydropyrimidase (EC 3.5.2.2)

β-ureidopropionase (EC 3.5.1.6)

Adenosine (to uric acid):

Adenosine deaminase (EC 3.5.4.4)

Purine nucleoside phosphorylase (EC 2.4.2.1)

Xanthine oxidase (EC 1.17.1.4; EC 1.17.3.2)

Guanosine (to uric acid):

Purine nucleoside phosphorylase (EC 2.4.2.1)

Guanine deaminase (EC 3.5.4.3)

Xanthine oxidase (EC 1.17.1.4; EC 1.17.3.2)


Amino acid biosynthesis

Alanine (from pyruvate):

Alanine transaminase (EC 2.6.1.2)

Alanine racemase (PLP-dependent) (EC 5.1.1.1)

Aspartate (from oxaloacetate):

Aspartate transaminase (EC 2.6.1.1)

Glutamate (from α-ketoglutarate):

Glutamate transaminase (EC 2.6.1.1)

Glutamine (from glutamate):

Glutamine synthase (EC 6.3.1.2)

Asparagine (from aspartate):

Asparagine synthase (EC 6.3.5.4)

Arginine (from glutamate via ornithine):

N-acetylglutamate synthase (EC 2.3.1.1)

Acetylglutamate kinase (EC 2.7.2.8)

*N-*acetyl-γ-glutamyl-phosphate reductase (1.2.1.38)

Acetylornithine transaminase (EC 2.6.1.11)

Acetylornithine deacetylase (EC 3.5.1.16)

then ornithine to arginine via urea cycle

Proline (from glutamate):

Glutamate-5-kinase (EC 2.7.2.11)

Glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41)

Pyrroline-5-carboxylate reductase (EC 1.5.1.2)

Serine (from 3-phosphoglycerate):

Phosphoglycerate dehydrogenase (EC 1.1.1.95)

Phosphoserine transaminase (EC 2.6.1.52)

Phosphoserine phosphatase (EC 3.1.3.3)

Cysteine (from serine):

Cystathionine β-synthase (EC 4.2.1.22)

Cystathionine γ-lyase (EC 4.4.1.1)

… or (in bacteria) :

O-acetylserine sulfhydrolase (EC 2.5.1.47)

Glycine (from serine):

Serine hydroxymethyltransferase (EC 2.1.2.1)

Lysine (from aspartate):

Aspartate kinase (EC 2.7.2.4) P16.3

Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Dihydrodipicolinate synthase (EC 4.2.1.52)

Dihydrodipicolinate reductase (EC 1.3.1.26)

Tetrahydropyridine-2-carboxylate N-succinyltransferase (EC 2.3.1.117)

Succinyl-diaminopimelate transaminase (EC 2.6.1.17)

Succinyl-diaminopimelate desuccinylase (EC 3.5.1.18)

Diaminopimelate decarboxylase (EC 4.1.1.20)

Methionine (from aspartate via homoserine):

Aspartate kinase (EC 2.7.2.4)

Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Homoserine dehydrogenase (EC 1.1.1.3)

Homoserine transsuccinylase (EC 2.3.1.46)

Cystathionine -synthase (EC 4.2.1.22)

Cystathionine β-lyase (EC 4.4.1.8)

Methionine synthase (EC 2.1.1.13)

Threonine (from homoserine):

Homoserine kinase (EC 2.7.1.39)

Threonine synthase (EC 4.2.3.1)

Isoleucine, leucine, valine (from pyruvate):

Acetolactate synthase (EC 2.2.1.6)

Ketol acid reductoisomerase (EC 1.1.1.86)

Dihydroxyacid dehydratase (EC 4.2.1.9)

Isoleucine:

Branched-chain-amino-acid transaminase (EC 2.6.1.42)

Valine:

Valine—pyruvate transaminase (EC 2.6.1.66)

Leucine:

2-isopropylmalate synthase (EC 2.3.3.13)

Isopropylmalate isomerase (EC 4.2.1.33)

3-isopropylmalate dehydrogenase (EC 1.1.1.85

Leucine transaminase (EC 2.6.1.6)

**
Aromatic amino acids**

Erythrose-4P to chorismate:

DAHP synthase (EC 2.5.1.54)

Dehydroquinate synthase (EC 4.2.3.4)

Dehydroquinate dehydratase (EC 4.2.1.10)

Shikimate dehydrogenase (EC 1.1.1.25)

shikimate kinase (EC 2.7.1.71) P10.2

5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (EC 2.5.1.19)

Chorismate synthase (EC 4.2.3.5)

Chorismate to tryptophan:

Anthranilate synthase (EC 4.1.3.27)

Anthranilate phosphoribosyltransferase (EC 2.4.2.18)

Phosphoribosyl anthranilate isomerase (EC 5.3.1.24)

Indole-3-glycerol phosphate synthase (EC 4.1.1.48)

Tryptophan synthase (EC 4.2.1.20)

Chorismate to phenylalanine/tyrosine

Chorismate mutase (EC 5.4.99.5)

Prephenate decarboxylase (EC 4.2.1.51)

Aromatic-amino-acid transaminase (EC 2.6.1.57)

Tyrosine transaminase (EC 2.6.1.5)

Histidine (from PRPP and ATP):

ATP phosphoribosyltransferase (EC 2.4.2.17)

Phosphoribosyl-ATP diphosphatase (EC 3..6.1.31)

Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16)

Imidazole glycerol-phosphate synthase (EC 4.3.1.B2)

Imidazoleglycerol-phosphate dehydratase (4.2.1.19)

Histidinol-phosphate transaminase (EC 2.6.1.9)

Histidinol-phosphatase (EC 3.1.3.15)

Histidinol dehydrogenase (EC 1.1.1.23)


Amino acid degradation

Transaminase (EC 2.6.1.1, EC 2.6.1.2)

Carbamoyl phosphate synthetase (EC 6.3.4.16)

Urea cycle

Ornithine transcarbamylase (EC 2.1.3.3)

Argininosuccinate synthetase (EC 6.3.4.5)

Arginosuccinate lyase (EC 4.3.2.1)

Arginase (EC 3.5.3.1)

Alanine (to pyruvate and glutamate):

Alanine transaminase (EC 2.6.1.2)

Serine

to pyruvate:

Serine dehydratase (EC 4.3.1.17)

to glycine:

Serine hydroxymethyltransferase (EC 2.1.2.1)

Glycine (glycine cleavage system):

Glycine dehydrogenase (decarboxylating) (EC 1.4.4.2)

Aminomethyltransferase (EC 2.1.2.10)

Cysteine (to pyruvate and SO2):

Cysteine dioxygenase (EC 1.13.11.20)

Aspartate transaminase (2.6.1.1)

Threonine

pathway 1 (to glycine and acetyl CoA):

Threonine dehydrogenase (EC 1.1.1.103)

Glycine C-acetyltransferase (EC 2.3.1.29)

pathway 2 (to glycine and acetaldehyde):

Threonine aldolase (EC 4.1.2.5)

pathway 3 (to succinyl-CoA via propionyl CoA):

Threonine dehydratase (EC 4.3.1.19)

2-oxobutanoate dehydrogenase (EC 1.2.4.4)

Propionyl-CoA carboxylase (EC 6.4.1.3)

Methylmalonyl-CoA mutase (EC 5.4.99.2)

**
Tryptophan** (to glutaryl-CoA):

Tryptophan 2,3-dioxygenase (EC 1.13.11.11)

Acylformamidase (EC 3.5.1.19)

Kynurenine 3-monooxygenase (EC 1.14.13.9)

Kynurenimase (EC 3.7.1.3)

3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6)

Aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45)

2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32)

2-aminomuconate deaminase (EC 3.5.99.5)

2-oxoglutarate dehydrogenase (EC 1.2.4.2)

Asparagine (to aspartate):

Asparaginase (EC 3.5.1.1)

Aspartate

to oxaloacetate:

Aspartate transaminase (EC 2.6.1.1)

to fumarate:

Aspartate-ammonia lyase (EC 4.3.1.1)

Glutamine (to glutamate):

Glutaminase (EC 3.5.1.2)

Glutamate (to α-ketoglutarate):

Glutamate dehydrogenase (EC 1.4.1.2)

Arginine (to glutamate):

Arginase (EC 3.5.3.1)

Ornithine transaminase (EC 2.6.1.13)

Glutamate semialdehyde dehydrogenase (EC 1.2.1.41)

Histidine (to glutamate):

Histidine ammonia-lyase (EC 4.3.1.3)

Urocanate hydratase (EC 4.2.1.49)

Imidazolonepropionase (EC 3.5.2.7)

Formimidoylglutamase (EC 3.5.3.8)

**
Valine, isoleucine, leucine:**

Branched chain amino acid transaminase (EC 2.6.1.42)

Branched chain ketoacid dehydrogenase complex (EC 1.2.4.4)

Acyl CoA dehydrogenase (eg. EC 1.3.99.13)

Valine (to succinyl CoA):

Enoyl-CoA hydratase (EC 4.2.1.17)

3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)

3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)

Methylmalonate-semialdehyde dehydrogenase (1.2.1.27)

Propionyl-CoA carboxylase (EC 6.4.1.3)

Methylmalonyl-CoA mutase (EC 5.4.99.2)

Isoleucine (to succinyl CoA and acetyl CoA)

Enoyl-CoA hydratase (EC 4.2.1.17)

Methyl-hydroxybutyryl CoA dehydrogenase (EC 1.1.1.178)

3-ketoacyl-CoA thiolase (EC 2.3.1.16)

Propionyl-CoA carboxylase (EC 6.4.1.3

Methylmalonyl-CoA mutase (EC 5.4.99.2)

Leucine (to acetyl CoA)

Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4)

Methylglutaconyl-CoA hydratase (EC 4.2.1.18)

Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)

Methionine (to cysteine and succinyl-CoA):

Methionine adenosyltransferase (EC 2.5.1.6)

Methyltransferase (eg. 2.1.1.37)

Adenosylhomocysteinase (EC 3.3.1.1)

Cystathionine beta-synthase (EC 4.2.1.22)

Cystathionine gamma-lyase (EC 4.4.1.1)

2-oxobutanoate dehydrogenase (EC 1.2.4.4)

Propionyl-CoA carboxylase (EC 6.4.1.3)

Methylmalonyl-CoA mutase (EC 5.4.99.2)

Lysine (to glutaryl-CoA):

Saccharopine dehydrogenase (EC 1.5.1.8)

Saccharopine reductase (EC 1.5.1.10)

Aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31)

2-aminoadipate transaminase (EC2.6.1.39)

2-oxoglutarate dehydrogenase (EC 1.2.4.2)

**
Phenylalanine** (to tyrosine):

Phenylalanine hydroxylase (EC 1.14.16.1)

Tyrosine (to fumarate and acetoacetate):

Tyrosine transaminase (EC 2.6.1.5)

4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Homogentisate 1,2-dioxygenase (EC 1.13.11.5)

Maleylacetoacetate isomerase (EC 5.2.1.2)

Fumarylacetoacetase (EC 3.7.1.2)

Appendix II: Review of core mechanism types

As you work through the chapters in the second half of this book, you should be sure that you can recognize and draw general examples of all of the following core mechanism types.

Section 8.1: Nucleophilic substitution: SN1 and SN2

Section 9.2: Phosphate transfer

Section 10.2:

Formation of hemiacetal/hemiketal

Collapse of hemiacetal/hemiketal

Section 10.3:

Formation of acetal/ketal

Hydrolysis of acetal/ketal

Section 10.4: N-glycosidic bond formation and hydrolysis

Section 10.5: Imine formation and hydrolysis

Section 11.2 Nucleophilic acyl substitution at carboxylic acid derivatives

Section 11.8: Nucleophilic substitution at activated amides and carbamides

Section 12.2:

Carbonyl regioisomerization

Racemization/epimerization at α-carbon

Alkene regioisomerization

Section 12.3: Aldol addition / retroaldol cleavage

Section 13.1: Decarboxylation

Section 13.3: Claisen condensation / retro-Claisen cleavage

Section 13.4:

Conjugate (Michael) addition

E1cb β-elimination

Section 13.5: Carboxylation

Section 14.1: Electrophilic addition to alkene

Section 14.2: E1 β-elimination

Section 14.3: Electrophilic isomerization

Section 14.4: Electrophilic substitution

Section 14.5: Carbocation rearrangement

Section 15.3:

Hydrogenation aldehyde/ketone/imine by NAD(P)H

Dehydrogenation of alcohol/amine by NAD(P)+

Section 15.4:

Hydrogenation of conjugated alkene by NAD(P)H or FADH2

Dehydrogenation of alkane by FAD

Section 15.6: Disulfide exchange

Section 16.2: Radical chain reactions