Cardiovascular biochemistry

Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1]

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Enzymes

Activity|

* Active site
* Binding site
* Catalytic triad
* Oxyanion hole
* Enzyme promiscuity
* Catalytically perfect enzyme
* Coenzyme
* Cofactor
* Enzyme catalysis

Regulation|

* Allosteric regulation
* Cooperativity
* Enzyme inhibitor
* Enzyme activator

Classification|

* EC number
* Enzyme superfamily
* Enzyme family
* List of enzymes

Kinetics|

* Enzyme kinetics
* Eadie–Hofstee diagram
* Hanes–Woolf plot
* Lineweaver–Burk plot
* Michaelis–Menten kinetics

Types|

* EC1 Oxidoreductases (list)
* EC2 Transferases (list)
* EC3 Hydrolases (list)
* EC4 Lyases (list)
* EC5 Isomerases (list)
* EC6 Ligases (list)

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Oxidoreductases: alcohol oxidoreductases (EC 1.1)

1.1.1: NAD/NADP acceptor|

* 3-hydroxyacyl-CoA dehydrogenase
* 3-hydroxybutyryl-CoA dehydrogenase
* Alcohol dehydrogenase
* Aldo-keto reductase
* 1A1
* 1B1
* 1B10
* 1C1
* 1C3
* 1C4
* 7A2
* Aldose reductase
* Beta-Ketoacyl ACP reductase
* Carbohydrate dehydrogenases
* Carnitine dehydrogenase
* D-malate dehydrogenase (decarboxylating)
* DXP reductoisomerase
* Glucose-6-phosphate dehydrogenase
* Glycerol-3-phosphate dehydrogenase
* HMG-CoA reductase
* IMP dehydrogenase
* Isocitrate dehydrogenase
* Lactate dehydrogenase
* L-threonine dehydrogenase
* L-xylulose reductase
* Malate dehydrogenase
* Malate dehydrogenase (decarboxylating)
* Malate dehydrogenase (NADP+)
* Malate dehydrogenase (oxaloacetate-decarboxylating)
* Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
* Phosphogluconate dehydrogenase
* Sorbitol dehydrogenase

* Hydroxysteroid dehydrogenase: 3β
* 3β-HSD
* NSDHL
* 11β
* 11β-HSD1
* 11β-HSD2
* 17β

1.1.2: cytochrome acceptor|

* D-lactate dehydrogenase (cytochrome)
* D-lactate dehydrogenase (cytochrome c-553)
* Mannitol dehydrogenase (cytochrome)

1.1.3: oxygen acceptor|

* Glucose oxidase
* L-gulonolactone oxidase
* Xanthine oxidase

1.1.4: disulfide as acceptor|

* Vitamin K epoxide reductase
* Vitamin-K-epoxide reductase (warfarin-insensitive)

1.1.5: quinone/similar acceptor|

* Malate dehydrogenase (quinone)
* Quinoprotein glucose dehydrogenase

1.1.99: other acceptors|

* Choline dehydrogenase
* L2HGDH

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Aldehyde/oxo oxidoreductases (EC 1.2)

1.2.1: NAD or NADP|

* Aldehyde dehydrogenase
* Acetaldehyde dehydrogenase
* Long-chain-aldehyde dehydrogenase

1.2.2: cytochrome|

* Formate dehydrogenase (cytochrome)

1.2.3: oxygen|

* Aldehyde oxidase

1.2.4: disulfide|

* Oxoglutarate dehydrogenase complex
* Pyruvate dehydrogenase
* Branched-chain alpha-keto acid dehydrogenase complex
* BCKDHA
* BCKDHB
* DBT
* DLD

1.2.7: iron-sulfur protein|

* Pyruvate synthase

* v
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Oxidoreductases: CH–CH oxidoreductases (EC 1.3)

1.3.1: NAD/NADP acceptor|

* Enoyl-acyl carrier protein reductase/Enoyl ACP reductase
* 7-Dehydrocholesterol reductase
* Biliverdin reductase
* 2,4 Dienoyl-CoA reductase
* Dihydroxymethyloxo-tetrahydroquinoline dehydrogenase

1.3.3: Oxygen acceptor|

* Dihydroorotate dehydrogenase
* Coproporphyrinogen III oxidase
* Protoporphyrinogen oxidase
* Bilirubin oxidase
* Acyl-CoA oxidase
* Dihydrouracil oxidase
* Tetrahydroberberine oxidase
* Secologanin synthase
* Tryptophan alpha,beta-oxidase
* Pyrroloquinoline-quinone synthase
* L-galactonolactone oxidase

1.3.5: Quinone|

* Succinate dehydrogenase
* SDHA
* SDHB
* SDHC
* SDHD

1.3.99: Other acceptors|

* Fumarate reductase
* Butyryl-CoA dehydrogenase
* Acyl CoA dehydrogenase
* ACADSB
* ACADS
* 5α-reductase
* SRD5A1
* SRD5A2
* SRD5A3
* Glutaryl-CoA dehydrogenase
* Isovaleryl coenzyme A dehydrogenase
* 3-oxo-5beta-steroid 4-dehydrogenase

* v
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CH-NH2 oxidoreductases (EC 1.4) - primarily amino acid oxidoreductases

1.4.1: NAD/NADP acceptor|

* Glutamate dehydrogenase
* GLUD1
* GLUD2
* Glutamate synthase (NADPH)

1.4.3: oxygen acceptor|

* D-amino acid oxidase
* Amine oxidase (Copper-containing (Lysyl
* Diamine
* Primary-amine)) (Flavin-containing (Monoamine)))

1.4.4: disulfide acceptor|

* Glycine cleavage system

1.4.99: other acceptors|

* D-amino acid dehydrogenase
* Amine dehydrogenase

* v
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Oxidoreductases: CH-NH (EC 1.5)

1.5.1: NAD or NADP acceptor|

* Dihydrofolate reductase
* Saccharopine dehydrogenase
* Methylenetetrahydrofolate reductase

1.5.3: oxygen acceptor|

* Dihydrobenzophenanthridine oxidase
* Sarcosine oxidase
* Proline oxidase

1.5.5: quinone acceptor|

* Electron-transferring-flavoprotein dehydrogenase

1.5.99|

* Sarcosine dehydrogenase
* Cytokinin dehydrogenase

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Oxidoreductases: NADH or NADPH (EC 1.6)

1.6.1: NAD/NADP|

* NAD(P)+ transhydrogenase (Si-specific)
* NAD(P)+ transhydrogenase (Re/Si-specific)

1.6.2: Heme|

* Methemoglobin reductase
* NADPH—hemoprotein reductase/Cytochrome P450 reductase
* NADPH—cytochrome-c2 reductase
* Leghemoglobin reductase

1.6.3: Oxygen|

* NADPH oxidase
* P91-PHOX
* Neutrophil cytosolic factor 1
* Neutrophil cytosolic factor 2
* Neutrophil cytosolic factor 4
* dual oxidase
* Dual oxidase 1
* Dual oxidase 2

1.6.5: Quinone or similar|

* NADH dehydrogenase

1.6.6: Nitrogenous group|

* Trimethylamine-N-oxide reductase

1.6.99: other|

* NADH dehydrogenase (quinone)

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Oxidoreductases: nitrogenous donor (EC 1.7)

1.7.1|

* GMP reductase

1.7.2|

* Nitrite reductase (NO-forming)

1.7.3|

* Urate oxidase

1.7.7|

* Ferredoxin—nitrite reductase

1.7.99|

* Hydroxylamine reductase

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Oxidoreductases: sulfur oxidoreductases (EC 1.8)

1.8.1: NAD or NADP|

* Dihydrolipoamide dehydrogenase
* Glutathione reductase
* Thioredoxin reductase

1.8.2: cytochrome|

* Sulfite dehydrogenase
* Thiosulfate dehydrogenase

1.8.3: oxygen|

* Sulfite oxidase

1.8.4: disulfide|

* Glutathione—homocystine transhydrogenase

1.8.5: quinone|

* Glutathione dehydrogenase (ascorbate)

1.8.98: Other, known|

* CoB—CoM heterodisulfide reductase

1.8.99: Other|

* Sulfite reductase

Template:Diphenol family oxidoreductases

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Oxidoreductases: peroxidases (EC 1.11)

1.11.1.1-14|

* NADH peroxidase
* NADPH peroxidase
* Fatty-acid peroxidase
* Catalase
* Cytochrome c peroxidase
* Eosinophil peroxidase
* Glutathione peroxidase
* GPX 1
* 2
* 3
* 4
* 5
* 6
* 7
* 8
* Horseradish peroxidase
* Lactoperoxidase
* Myeloperoxidase
* Thyroid peroxidase
* Deiodinase
* Iodothyronine deiodinase
* Iodotyrosine deiodinase

1.11.1.15 (peroxiredoxin)|

* 1
* 2
* 3
* 4
* 5
* 6

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Oxidoreductases: monooxygenases (EC 1.13)

1.13.11: two atoms of oxygen|

* lipoxygenase: Arachidonate 5-lipoxygenase
* Arachidonate 12-lipoxygenase/ALOX12
* Arachidonate 8-lipoxygenase
* Arachidonate 15-lipoxygenase/ALOX15
* Linoleate 11-lipoxygenase

* other dioxygenase: Catechol dioxygenase
* Homogentisate 1,2-dioxygenase
* Cysteine dioxygenase
* 4-Hydroxyphenylpyruvate dioxygenase
* Indoleamine 2,3-dioxygenase
* Chlorite dismutase

1.13.12: one atom of oxygen|

* Firefly luciferase

1.13.99: other|

* Inositol oxygenase

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Oxidoreductases: dioxygenases, including steroid hydroxylases (EC 1.14)

1.14.11: 2-oxoglutarate|

* Prolyl hydroxylase
* Lysyl hydroxylase

1.14.13: NADH or NADPH|

* Flavin-containing monooxygenase
* FMO1
* FMO2
* FMO3
* FMO4
* FMO5
* Nitric oxide synthase
* NOS1
* NOS2
* NOS3
* Cholesterol 7 alpha-hydroxylase
* Methane monooxygenase
* 3A4
* Lanosterol 14 alpha-demethylase
* 24-hydroxycholesterol 7α-hydroxylase

1.14.14: reduced flavin or flavoprotein|

* 19A1
* 2D6
* 2E1

1.14.15: reduced iron-sulfur protein|

* 11B1
* 11B2
* 11A1

1.14.16: reduced pteridine (BH4 dependent)|

* Phenylalanine hydroxylase
* Tyrosine hydroxylase
* Tryptophan hydroxylase

1.14.17: reduced ascorbate|

* Dopamine beta-hydroxylase

1.14.18-19: other|

* Tyrosinase
* Stearoyl-CoA desaturase-1

1.14.99 \- miscellaneous|

* Cyclooxygenase
* Heme oxygenase (HMOX1)
* Squalene monooxygenase
* 17A1
* 21A2

* v
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Other oxidoreductases (EC 1.15-1.21)

1.15: Acting on superoxide as acceptor|

* Superoxide dismutase
* SOD1
* SOD2
* SOD3

1.16: Oxidizing metal ions|

* Ceruloplasmin

1.17: Acting on CH or CH2 groups|

* Xanthine oxidase
* Ribonucleotide reductase
* 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase

1.18: Acting on iron-sulfur proteins as donors|

* Nitrogenase

1.19: Acting on reduced flavodoxin as donor|

* Nitrogenase (flavodoxin)

1.20: Acting on phosphorus or arsenic in donors|

* Glutaredoxin
* GLRX
* GLRX2
* GLRX3
* GLRX5

1.21: Acting on X-H and Y-H to form an X-Y bond|

* Isopenicillin N synthase
* Columbamine oxidase
* Reticuline oxidase
* Sulochrin oxidase
* (+)-bisdechlorogeodin-forming
* (-)-bisdechlorogeodin-forming
* Aureusidin synthase
* Tetrahydrocannabinolic acid synthase
* Cannabidiolic acid synthase
* Dichlorochromopyrrolate synthase

* v
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Transferases: phosphorus-containing groups (EC 2.7)

2.7.1-2.7.4:
phosphotransferase/kinase
(PO4)|

| 2.7.1: OH acceptor|

* Hexo-
* Gluco-
* Fructo-
* Hepatic
* Galacto-
* Phosphofructo-
* 1
* Liver
* Muscle
* Platelet
* 2
* Riboflavin
* Shikimate
* Thymidine
* ADP-thymidine
* NAD+
* Glycerol
* Pantothenate
* Mevalonate
* Pyruvate
* Deoxycytidine
* PFP
* Diacylglycerol
* Phosphoinositide 3
* Class I PI 3
* Class II PI 3
* Sphingosine
* Glucose-1,6-bisphosphate synthase

|

2.7.2: COOH acceptor|

* Phosphoglycerate
* Aspartate kinase

2.7.3: N acceptor|

* Creatine

2.7.4: PO4 acceptor|

* Phosphomevalonate
* Adenylate
* Nucleoside-diphosphate
* Uridylate
* Guanylate
* Thiamine-diphosphate

2.7.6: diphosphotransferase
(P2O7)|

* Ribose-phosphate diphosphokinase
* Thiamine diphosphokinase

2.7.7: nucleotidyltransferase
(PO4-nucleoside)|

| Polymerase|

| DNA polymerase|

DNA-directed DNA polymerase

III

RNA-directed DNA polymerase
Reverse transcriptase

Telomerase

DNA nucleotidylexotransferase/Terminal deoxynucleotidyl transferase

|

RNA nucleotidyltransferase|

RNA polymerase/DNA-directed RNA polymerase
RNA polymerase I

III

Primase
RNA-dependent RNA polymerase

PNPase

Phosphorolytic
3' to 5' exoribonuclease|

* RNase PH
* PNPase

Nucleotidyltransferase|

* UTP—glucose-1-phosphate uridylyltransferase
* Galactose-1-phosphate uridylyltransferase

Guanylyltransferase|

* mRNA capping enzyme

Other|

* Recombinase (Integrase)
* Transposase

2.7.8: miscellaneous|

| Phosphatidyltransferases|

* CDP-diacylglycerol—glycerol-3-phosphate 3-phosphatidyltransferase
* CDP-diacylglycerol—serine O-phosphatidyltransferase
* CDP-diacylglycerol—inositol 3-phosphatidyltransferase
* CDP-diacylglycerol—choline O-phosphatidyltransferase

|

Glycosyl-1-phosphotransferase|

* N-acetylglucosamine-1-phosphate transferase

2.7.10-2.7.13: protein kinase
(PO4; protein acceptor)|

| 2.7.10: protein-tyrosine|

* see tyrosine kinases

|

2.7.11: protein-serine/threonine|

* see serine/threonine-specific protein kinases

2.7.12: protein-dual-specificity|

* see serine/threonine-specific protein kinases

2.7.13: protein-histidine|

* Protein-histidine pros-kinase
* Protein-histidine tele-kinase
* Histidine kinase

* v
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Transferase: one carbon transferases (EC 2.1)

2.1.1 - Methyltransferases|

5-hydroxyindole-O-methyltransferase/Acetylserotonin O-methyltransferase \- Betaine-homocysteine methyltransferase \- Catechol-O-methyl transferase \- Histamine N-methyltransferase \- Homocysteine methyltransferase \- 5-Methyltetrahydrofolate-homocysteine methyltransferase \- Phosphatidyl ethanolamine methyltransferase \- Phenylethanolamine N-methyltransferase \- DNMT3B \- Histone methyltransferase \- Thymidylate synthase \- Tryptamine N-methyltransferase \- DNA methyltransferase

2.1.2 - Hydroxy methyl-, Formyl\- and Related Transferases|

Serine hydroxymethyltransferase \- Phosphoribosylglycinamide formyltransferase \- Inosine monophosphate synthase \- Glutamate formimidoyltransferase \- Aminomethyltransferase

2.1.3 - Carboxy\- and Carbamoyl transferases|

Ornithine transcarbamylase

2.1.4 - Amidino transferases|

Arginine:glycine amidinotransferase

* v
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Transferases: aldehyde-ketone (EC 2.2)

2.2.1|

* Acetolactate synthase
* Transaldolase
* Transketolase
* DXP synthase

* v
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* e

Transferases: acyltransferases (EC 2.3)

2.3.1: other than amino-acyl groups|

* acetyltransferases: Acetyl-Coenzyme A acetyltransferase
* N-Acetylglutamate synthase
* Choline acetyltransferase
* Dihydrolipoyl transacetylase
* Acetyl-CoA C-acyltransferase
* Beta-galactoside transacetylase
* Chloramphenicol acetyltransferase
* N-acetyltransferase
* Serotonin N-acetyl transferase
* HGSNAT
* ARD1A
* Histone acetyltransferase
* P300/CBP
* NAT2

* palmitoyltransferases: Carnitine O-palmitoyltransferase
* CPT1
* CPT2
* Serine C-palmitoyltransferase
* SPTLC1
* SPTLC2

* other: Acyltransferase like 2
* Aminolevulinic acid synthase
* Beta-ketoacyl-ACP synthase
* Glyceronephosphate O-acyltransferase
* Lecithin—cholesterol acyltransferase

* Glycerol-3-phosphate O-acyltransferase
* 1-acylglycerol-3-phosphate O-acyltransferase
* 2-acylglycerol-3-phosphate O-acyltransferase
* ABHD5

2.3.2: Aminoacyltransferases|

* Gamma-glutamyl transpeptidase
* Peptidyl transferase
* Transglutaminase
* Tissue transglutaminase
* Keratinocyte transglutaminase
* Factor XIII

2.3.3: converted into alkyl on transfer|

* Citrate synthase
* ATP citrate lyase
* HMG-CoA synthase
* Malate synthase

* v
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Transferases: glycosyltransferases (EC 2.4)

2.4.1: Hexosyl-
transferases|

| Glucosyl-|

* Phosphorylase
* Starch
* Glycogen
* Myo-
* Glycogen synthase
* Debranching enzyme
* Branching enzyme
* 1,3-Beta-glucan synthase
* Ceramide glucosyltransferase
* N-glycosyltransferase

|

Galactosyl-|

* Lactose synthase
* B-N-acetylglucosaminyl-glycopeptide b-1,4-galactosyltransferase
* Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase (C1GALT1)

Glucuronosyl-|

* B3GAT1
* B3GAT2
* B3GAT3

* UGT1A1
* UGT1A3
* UGT1A4
* UGT1A5
* UGT1A6
* UGT1A7
* UGT1A8
* UGT1A9
* UGT1A10

* UGT2A1
* UGT2A2
* UGT2A3
* UGT2B4
* UGT2B7
* UGT2B10
* UGT2B11
* UGT2B15
* UGT2B17
* UGT2B28

* Hyaluronan synthase: HAS1
* HAS2
* HAS3

Fucosyl-|

* POFUT1
* POFUT2
* FUT1
* FUT2
* FUT3
* FUT4
* FUT5
* FUT6
* FUT7
* FUT8
* FUT9
* FUT10
* FUT11

Mannosyl-|

* Dolichyl-phosphate-mannose-protein mannosyltransferase
* POMT1
* POMT2
* DPM1
* DPM3

* ALG1
* ALG2
* ALG3
* ALG6
* ALG8
* ALG9
* ALG12

2.4.2: Pentosyl-
transferases|

| Ribose|

| ADP-ribosyltransferase|

* NAD+:diphthamide ADP-ribosyltransferase
* Diphtheria toxin

* NAD(P)+:arginine ADP-ribosyltransferase
* Pertussis toxin
* Cholera toxin

* Poly ADP ribose polymerase

* Sirtuin

|

Phosphoribosyltransferase|

* Adenine phosphoribosyltransferase
* Hypoxanthine-guanine phosphoribosyltransferase
* Uracil phosphoribosyltransferase
* Amidophosphoribosyltransferase

Other|

* Purine nucleoside phosphorylase: Thymidine phosphorylase
* ECGF1

Other|

* Xylosyltransferase
* XYLT1
* XYLT2
* Arabinosyltransferase
* Indolylacetylinositol arabinosyltransferase

2.4.99: Sialyl
transferases|

* Beta-galactoside alpha-2,6-sialyltransferase
* Monosialoganglioside sialyltransferase
* ST8SIA4

* v
* t
* e

Transferases: alkyl and aryl (EC 2.5)

2.5.1|

* Dimethylallyltranstransferase
* Thiaminase I
* Methionine adenosyltransferase
* Riboflavin synthase
* Dihydropteroate synthase
* Spermidine synthase
* Glutathione S-transferase
* Farnesyl-diphosphate farnesyltransferase
* Spermine synthase
* Alkylglycerone phosphate synthase
* Farnesyltransferase
* Geranylgeranyltransferase type 1
* Porphobilinogen deaminase

* v
* t
* e

Transferase: nitrogenous groups (EC 2.6)

2.6.1: Transaminases|

* Aspartate transaminase
* GOT1
* GOT2
* Alanine transaminase
* GABA transaminase
* Tyrosine aminotransferase
* Kynurenine—oxoglutarate transaminase
* Ornithine aminotransferase
* Branched-chain amino acid aminotransferase
* Alanine—glyoxylate transaminase
* AGXT

2.6.3: Oximinotransferases|

* Oximinotransferase

2.6.99: Other|

* Pyridoxine 5'-phosphate synthase

Template:Phosphotransferases

* v
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* e

Transferases: sulfur-containing group (EC 2.8)

2.8.1: Sulfurtransferases|

* Thiosulfate sulfurtransferase
* Rhodanese
* 3-mercaptopyruvate sulfurtransferase
* thiosulfate—thiol sulfurtransferase
* tRNA sulfurtransferase
* thiosulfate—dithiol sulfurtransferase
* biotin synthase
* cysteine desulfurase

2.8.2: Sulfotransferases|

* Alcohol sulfotransferase
* Tyrosylprotein sulfotransferase
* Aryl sulfotransferase

2.8.3: CoA-transferases|

* Propionate CoA-transferase

2.8.4: Alkylthio|

* Coenzyme-B sulfoethylthiotransferase

* v
* t
* e

Enzymes: CO CS and CN ligases (EC 6.1-6.3)

6.1: Carbon-Oxygen|

* Aminoacyl tRNA synthetase
* Alanine
* Arginine
* Asparagine
* Aspartate
* Cysteine
* D-alanine—poly(phosphoribitol) ligase
* Glutamate
* Glutamine
* Glycine
* Histidine
* Isoleucine
* Leucine
* Lysine
* Methionine
* Phenylalanine
* Proline
* Serine
* Threonine
* Tryptophan
* Tyrosine
* Valine

6.2: Carbon-Sulfur|

* Succinyl coenzyme A synthetase
* Acetyl—CoA synthetase
* Long-chain-fatty-acid—CoA ligase

6.3: Carbon-Nitrogen|

* Glutamine synthetase
* Ubiquitin ligase
* Cullin
* Von Hippel–Lindau tumor suppressor
* UBE3A
* Mdm2
* Anaphase-promoting complex
* UBR1
* Glutathione synthetase
* CTP synthetase
* Adenylosuccinate synthase
* Argininosuccinate synthase
* Holocarboxylase synthetase
* GMP synthase
* Asparagine synthetase
* Carbamoyl phosphate synthetase
* I
* II
* Glutamate–cysteine ligase

* v
* t
* e

Ligases: carbon-carbon ligases (EC 6.4)

Biotin dependent carboxylation|

* Pyruvate carboxylase
* Acetyl-CoA carboxylase
* Propionyl-CoA carboxylase
* Methylcrotonyl-CoA carboxylase

Other|

* Polyketide synthase

* v
* t
* e

Enzymes: Phosphoric ester and nitrogen-metal ligases (EC 6.5-6.6)

6.5: Phosphoric Ester|

* DNA ligase

6.6: Nitrogen-Metal|

* Magnesium chelatase
* Cobalt chelatase

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