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Andy Howard Biochemistry Lectures, Spring April 2019

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1 Andy Howard Biochemistry Lectures, Spring 2019 18 April 2019
Lipid Anabolism Andy Howard Biochemistry Lectures, Spring April 2019

2 Lipids are synthesized and broken down
We begin to explore anabolic and catabolic systems other than carbohydrates Fatty acid synthesis is a well-understood system Synthesis of other lipids can be intricate and complex Breakdown yields energy and reducing equivalents 04/18/2019 Lipid Anabolism

3 What we’ll discuss Lipid Anabolism Overview Fatty acids
Phospholipids & triglycerides Arachidonate Sphingolipids Isoprenoids and Steroids 04/18/2019 Lipid Anabolism

4 Lipid Anabolism Malonyl CoA Generally the starting point for building up lipids are acetyl CoA and malonyl CoA, and their variants acetyl ACP and malonyl ACP These are energy-requiring reactions: the compounds we’re making are reduced CF&M §21.6 04/18/2019 Lipid Anabolism

5 Acetoacetyl Acyl Carrier Protein
Overview Bacteria: acetyl CoA + malonyl ACP  acetoacetyl ACP + CO2 + CoASH Eukaryotes: acetyl CoA + ACP  acetyl ACP + CoASH acetyl ACP + malonyl ACP  acetoacetyl ACP + CO2 + ACP 04/18/2019 Lipid Anabolism

6 Acyl carrier protein Acts as a template on which acyl chain elongation can occur Attachment via phosphopantatheine group as with CoA; attaches at Ser 36 Simple protein: 77 amino acids, mostly helical, Zn2+-dependent E. Coli ACP 8.5 kDa monomer PDB 1T8K 04/18/2019 Lipid Anabolism

7 PDB 1W96 (biotin carboxylase domain)
183 kDa trimer Yeast EC , 1.8Å Making malonyl CoA Acetyl CoA incorporates an extra carboxyl via acetyl CoA carboxylase (ACC): HCO3- + ATP + acetyl CoA  ADP + Pi + malonyl CoA Biotin- and ATP-dependent ligase enzyme; similar to pyruvate carboxylase 1UYR (carboxyl-transferase domain), 2.5Å 162 kDa dimer; yeast 04/18/2019 Lipid Anabolism

8 Making malonyl ACP Malonyl CoA:ACP transacylase transfers the malonate group from coenzyme A to the acyl carrier protein Ferredoxin-like protein:  sandwich plus  sandwich Similar enzyme converts acetyl CoA to acetyl ACP E.coli Malonyl CoA: ACP transacylase E.C PDB 1MLA, 1.5Å 32kDa monomer 04/18/2019 Lipid Anabolism

9 Initiation reaction We want to start with a four-carbon unit attached to acyl carrier protein Condense acetyl CoA or acetyl ACP with malonyl ACP with ketoacyl ACP synthase (KAS) to form acetoacetyl ACP Intermediate has KAS covalently attached to both substrates Decarboxylation of enzyme-bound intermediates leads to 4-carbon unit attached to ACP  1 + 4 04/18/2019 Lipid Anabolism

10 Is this typical? Yes! We’ve carboxylated acetyl CoA to make malonyl ACP and then decarboxylated the product of malonyl ACP with acetyl CoA / ACP This provides a favorable free- energy change (at the expense of ATP) for the overall reaction Similar approach happens in gluconeogenesis (pyruvate  oxaloacetate  PEP) E.coli Ketoacyl ACP synthase PDB 1HNJ 70 kDa dimer; monomer shown EC , 1.46Å 04/18/2019 Lipid Anabolism

11 Elongations in FA synthesis: overview
Acetoacetyl ACP: starting point for elongations Pattern in each elongation is reduction  dehydration  reduction, resulting in a saturated product 04/18/2019 Lipid Anabolism

12 What happens next? Result reenters the pathway by condensing with malonyl ACP Elongated product plays the same role that acetyl CoA or acetyl ACP plays in the initial -ketoacyl ACP synthase reaction: C2n + C3  CO2 + C2n+2 04/18/2019 Lipid Anabolism

13 1st step: reduce ketone  sec-alcohol
Enzyme:3-ketoacyl ACP reductase (“KR”) Ketone reacts with NADPH + H+ to produce sec-alcohol + NADP+ D-isomer of sec-alcohol always forms; during degradation, L-isomer forms Enzyme is typical NAD(P)-dependent oxidoreductase PDB 2C kDa tetramer; Monomer shown Plasmodium falciparum EC , 1.5Å 04/18/2019 Lipid Anabolism

14 2nd step: alcohol to enoyl ACP (DH)
3-hydroxyacyl ACP dehydratase Eliminates water at beta, alpha positions to produce trans-2-enoyl ACP: R–CHOH–CH2-CO-S-ACP  R–CH=CH–CO-S-ACP + H2O PDB 1DCI 182 kDa hexamer trimer shown Rat mitochondria EC , 1.5Å 04/18/2019 Lipid Anabolism

15 Product and enzyme Note that the product is a derivative of a trans-fatty acid; but it’s complexed to ACP! This form of dehydratase is primarily helical; there is an alternative found in Aeromonas that is an alpha-beta roll structure 04/18/2019 Lipid Anabolism

16 3rd step: enoyl ACP to saturated ACP (ER)
PDB 2Z6I 73 kDa dimer Streptococcus pneumoniae EC , 1.7Å Enzyme: enoyl-ACP reductase Leaves behind fully saturated FA complexed to acyl carrier protein: R–CH=CH–CO-S-ACP + NADPH + H+  R–CH2CH2CO-S-ACP + NADP+ 04/18/2019 Lipid Anabolism

17 Decarboxylation and lengthening
This can then condense with malonyl ACP with decarboxylation to form longer beta-ketoacyl ACP: R2n-ACP + malonyl-ACP  -keto-R2n+2-ACP + CO2 + ACP-SH Enzyme is FMN-dependent 04/18/2019 Lipid Anabolism

18 How does this end? Generally starts at C4 and goes to C16 or C18.
Condensing enzyme won’t fit longer FAs Completed fatty acid is cleaved from ACP by action of a thioesterase (TE) with a 3-layer Rossmann fold Palmitoyl thioesterase I PDB 1EI9 31 kDa monomer bovine EC , 2.25Å 04/18/2019 Lipid Anabolism

19 The overall reaction Acetyl CoA + 7 Malonyl CoA + 14NADPH + 14 H+  14 NADP + + Palmitate + 7CO2 + 8HS-CoA + 6H2O In bacteria we have separate enzymes: a type II fatty acid synthesis system In animals we have a type I FA synthesis system: a large, multi-functional enzyme including the phosphopantatheine group by which the ACP attaches 04/18/2019 Lipid Anabolism

20 Activating fatty acids
Activate stearate or palmitate via acyl CoA synthetase: R–COO- + CoASH + ATP  R–CO–SCoA + AMP + PPi As usual, PPi hydrolysis drives the reaction to the right PLP-dependent reaction E.coli acyl CoA synthetase EC kDa monomer PDB 1BS0 04/18/2019 Lipid Anabolism

21 Differences among synthases
Bacteria have one acyl CoA synthetase Mammals: four isozymes for different FA lengths (small, medium, long, very long) Human medium chain acyl CoA synthetase EC kDa monomer PDB 3C5E, 1.6Å 04/18/2019 Lipid Anabolism

22 Extending and unsaturating fatty acids
There are applications for FAs with more than 18 carbons and FAs with ≥ 1 cis double bonds Elongases and desaturases handle these needs Desaturase adds a cis-double bond; if the FA already has unsaturations, the new one is added three carbons closer to the carboxyl Elongases condense FA with malonyl CoA; decarboxylation means we add two carbons 04/18/2019 Lipid Anabolism

23 Bacterial Desaturases
Acyl ACP desaturases in bacteria simply add a cis double bond in place of the normal trans double bond at the second phase of elongation; the cis double bond thus created remains during subsequent rounds Ferritin-like structure Mycobacterium tuberculosis Acyl ACP desaturase EC kDa monomer PDB 1ZA0, 2Å 04/18/2019 Lipid Anabolism

24 Eukaryotic Desaturases
Desaturases like stearoyl ACP desaturase in eukaryotes act on the completed saturated fatty acyl CoA species Enzyme is ferritin-like or RNR-like Mammals can’t synthesize linoleate and they need it, so it has to be part of the diet Castor bean stearoyl ACP desaturase 80 kDa dimer monomer shown EC , PDB 1OQ9, 2.4Å 04/18/2019 Lipid Anabolism

25 Making arachidonate Convert dietary linoleate to arachidonyl CoA via desaturation & elongations The fact that the new double bonds start 3 carbons away from the previous one means they’re not conjugated 04/18/2019 Lipid Anabolism

26 iClicker question 1 1. An appropriate summary of each lengthening step in eukaryotic fatty acid biosynthesis is (a) C2nCoA + acetylCoA → C2n+2CoA + CoASH (b) C2nACP + acetylACP → C2n+2ACP+ ACP (c) C2nACP + malonyl ACP → C2n+2ACP + CO2 + ACP (d) none of the above 04/18/2019 Lipid Anabolism

27 Phosphatidates Phosphatidates are intermediates in making triacylglycerol & glycerophospholipids Fatty acyl groups esterifying 1 and 2 positions of glycerol, phosphate esterifying 3 position CF&M §21.7 04/18/2019 Lipid Anabolism

28 Making phosphatidates
Glycerol-3-phosphate acyltransferase transfers acyl CoA to 1 position of glycerol-3-phosphate; prefers saturated chains Glycerol-3-P acyltransferase 40 kDa monomer Cucurbita EC PDB 1IUQ , 1.55Å 04/18/2019 Lipid Anabolism

29 Second part of the step 1-acylglycerol-3-phosphate acyl transferase transfers acyl CoA to 2 position of resulting molecule; prefers unsaturated chains 04/18/2019 Lipid Anabolism

30 Making triacylglycerols and phospholipids
Phosphatidate phosphatase gets rid of the phosphate at the 3 position by hydrolysis to make 1,2-diacylglycerol A bit counterintuitive in making phospholipids: why get rid of the phosphate when you’re going to put a phosphorylated compound back at 3 position? But the groups you add already have phosphate on them! 04/18/2019 Lipid Anabolism

31 Further steps in making triacylglycerols
Diacylglycerol acyltransferase catalyzes reaction between 1,2-diacylglycerol and acyl CoA to form triacylglycerol Drug target for drug-resistant Mycobacterium tuberculosis strains M. tuberculosis Diacylglycerol acyltransferase with Ebselen EC kDa monomer PDB 4MQM, 1.35Å 04/18/2019 Lipid Anabolism

32 Making phospholipids from 1,2-diacylglycerol
1,2-diacylglycerol reacts with CDP-choline to form phosphatidylcholine with liberation of cytidine monophosphate 1,2-diacylglycerol reacts with CDP-ethanolamine to form phosphatidylethanolamine this can be methylated 3 times to make phosphatidylcholine S-adenosylmethionine is methyl donor here 04/18/2019 Lipid Anabolism

33 How do we get CDP-alcohols?
CDP-ethanolamine Easy: CTP + alcohol phosphate  CDP-alcohol + PPi As usual, reaction is driven to the right by hydrolysis of PPi Enzymes are CTP:phosphoethanolamine cytidylyltransferase and CTP:phosphocholine cytidylyltransferase 04/18/2019 Lipid Anabolism

34 Making acidic phospholipids
CDP-diacylglycerol Making acidic phospholipids Phosphatidate activated to CDP-diacylglycerol as catalyzed by CTP:phosphatidate cytidylyltransferase with release of PPi (see previous reactions) 04/18/2019 Lipid Anabolism

35 CDP-diacylglycerol reactivity
CDP-diacylglycerol can react with serine or inositol to form the relevant phospholipids This route to phosphatidylserine is found only in bacteria 04/18/2019 Lipid Anabolism

36 Bacterial approach Phosphatidylserine synthase: CDP-diacylglycerol + serine  CMP + phosphatidylserine Illustrates the fact that each of the four RNA nucleotides has its own special role in biosynthesis Haemophilus PS synthase 161kDa homotrimer EC PDB 3HSI, 2.2Å 04/18/2019 Lipid Anabolism

37 Phosphatidylserine and phosphatidylethanolamine
04/18/2019 Lipid Anabolism

38 Phosphatidylinositol
Phosphatidylinositol is made by this CDP-diacylglycerol pathway in bacteria and eukaryotes 04/18/2019 Lipid Anabolism

39 Making phosphatidylserine
Alternative approach to phosphatidylserine found in eukaryotes: make phosphatidylethanolamine, then phosphatidylethanolamine:serine transferase swaps serine for ethanolamine Thus we recover phosphoethanolamine back by a decarboxylation (or another exchange) Ethanolamine is just serine without COO- ! 04/18/2019 Lipid Anabolism

40 Where does this happen? Mostly in the endoplasmic reticulum in eukaryotes Biosynthesis enzymes are membrane bound but have their active sites facing the cytosol so they can pick up the water-soluble metabolites from which they can build up phospholipids and other lipids 04/18/2019 Lipid Anabolism

41 iClicker question #2 2. Phosphatidylserine and phosphatidylinositol are considered (a) anionic phospholipids (b) cationic phospholipids (c) neutral phospholipids (d) none of the above 04/18/2019 Lipid Anabolism

42 iClicker question #3 (a) anionic phospholipids
3. Phosphatidylcholine and phosphatidylethanolamine are considered (a) anionic phospholipids (b) cationic phospholipids (c) neutral phospholipids (d) none of the above 04/18/2019 Lipid Anabolism

43 Making eicosanoids Classes of eicosanoids:
Prostaglandins and thromboxanes Leukotrienes Remember that we make arachidonate from linoleoyl CoA; eiconsanoids are made from arachidonate Reactions involve formation of oxygen-containing rings; thus the enzymes are cyclooxygenases 04/18/2019 Lipid Anabolism

44 What eiconsanoids do They’re like hormones, but they act very locally: within µm of the cell in which they’re produced Involved in platelet aggregation, blood clots, constriction of smooth muscles Mediate pain sensitivity, inflammation, swelling Therefore enzymes that interconvert them are significant drug targets! 04/18/2019 Lipid Anabolism

45 Synthesizing prostaglandins
Prostaglandin H2 Synthesizing prostaglandins Prostaglandin H synthase (PGHS) binds on inner surface of ER Cyclooxygenase activity makes a hydroperoxide; this is converted to PGH2 PGH2 gets converted to other prostaglandins, prostacyclin, thromboxane A2 Sheep PGHS 132 kDa dimer EC PDB 1Q4G, 2.0Å 04/18/2019 Lipid Anabolism

46 How aspirin works Aspirin irreversibly inhibits the COX activity of PGHS by transferring an acetyl group to an active-site Ser That blocks eiconsanoid production, which reduces swelling and pain But there are side effects because some PGHS isozymes are necessary 04/18/2019 Lipid Anabolism

47 Cyclooxygenase inhibition
Cox-1 is constitutive: regulates secretion of mucin in the stomach Cox-2 is inducible: promotes inflammation, pain, fever Aspirin inhibits both: mucin-secretion inhibition means that causes bleeding or ulcers in the stomach lining Other nonsteroidal anti-inflammatories (NSAIDs) besides aspirin compete with arachidonate rather than binding covalently to COX-1 and COX-2 04/18/2019 Lipid Anabolism

48 Could we find a COX-2 inhibitor?
rofecoxib Could we find a COX-2 inhibitor? This would eliminate aspirin’s stomach irritation Structure-based inhibitors have been developed They work as expected; but They also increase risk of cardiovascular disease 04/18/2019 Lipid Anabolism

49 Leukotrienes Leukotriene B4
Lipoxygenases convert arachidonate to these compounds, which contain 3 conjugated double bonds These compounds interact with GPCRs Inflammatory and allergic reactions Involved in pathophysiology of asthma rabbit lipoxygenase 146 kDa dimer EC PDB 2P0M, 2.4Å 04/18/2019 Lipid Anabolism

50 Synthesis of ether lipids
Remember: these are lipids with ether linkages instead of acyl linkages Begins with dihydroxyacetone phosphate Acyltransferase acylates DHAP C-1 1-alkyl-DHAP synthase swaps an alcohol for the acyl group at C-1 Keto group at C2 of 1-alkyl-DHAP is reduced to an alcohol (NADPH-dependent reaction) 04/18/2019 Lipid Anabolism

51 Ether lipids, continued
1-alkylglycerophosphate acyltransferase adds another acyl group at C-2 Dephosphorylated at C-3 (as with phospholipids … take the P off, put it back on …) 04/18/2019 Lipid Anabolism

52 Remaining ether phospholipid steps
Phosphocholine or other phosphate-based ligand added at C-3 Plasmalogens earn a double bond between the two carbons adjacent to the ether oxygen on C-1 04/18/2019 Lipid Anabolism

53 Sphingolipid synthesis
ceramide Sphingolipid synthesis ceramide These are based formally on sphingosine, a C18 unsaturated amino alcohol Condense serine with palmitoyl CoA to make 3-ketosphinganine and CO2 NADPH-reduce this to sphinganine 04/18/2019 Lipid Anabolism

54 Subsequent steps to ceramide
Acetylate the amine group to make N-acylsphinganine Beta-unsaturate the palmitoyl group to make ceramide, the basis for all other sphingolipids 04/18/2019 Lipid Anabolism

55 Serine palmitoyl-transferase
Catalyzes 1st step in this pathway: Serine + palmitoyl CoA  3-ketodihydrosphingosine + CO2 + CoASH Can accept other amino acids as substrates PLP-dependent enzyme Sphingomonas paucimobilis SPT EC kDa dimer; monomer shown PDB 2JG2, 1.3Å 04/18/2019 Lipid Anabolism

56 Other sphingolipids sphingomyelin
React ceramide with phosphatidylcholine; products are sphingomyelin and 1,2-diacylglycerol React ceramide with UDP-galactose to form a galactocerebroside Additional UDP-sugars or CMP-N-acetyl-neuraminic acid can be added 04/18/2019 Lipid Anabolism

57 Steroid synthesis: overview
Cholesterol is important on its own & as a precursor of steroid hormones, bile salts Derived formally from isoprene Isoprenoid synthesis based on mevalonate & isopentenyl diphosphate 04/18/2019 Lipid Anabolism

58 Making HMG-CoA Condense 3 molecules of acetyl CoA:
2 acetyl CoA  acetoacetyl CoA + CoASH; catalyzed by acetoacetyl CoA synthase Acetoacetyl CoA + acetyl CoA + H2O  3-hydroxy-3-methylglutaryl CoA + CoASH + H+ catalyzed by HMG CoA synthase 04/18/2019 Lipid Anabolism

59 HMG-CoA and precursors
These are important intermediates: precursor to steroids and ketone bodies Not the committed step toward steroids because we can also make ketone bodies from HMG-CoA 04/18/2019 Lipid Anabolism

60 HMG CoA synthase Acetyl CoA + acetoacetyl CoA  HMG CoA + CoASH
Cytosolic and mitochondrial forms are different Human Mitochondrial HMG CoA synthase PDB 2WYA 105 kDa dimer EC , 1.7Å 04/18/2019 Lipid Anabolism

61 Distinctions between the two
Cytosolic forms are primarily used for isoprenoid synthesis leading to steroids Mitochondrial form is primarily used in making ketone bodies 04/18/2019 Lipid Anabolism

62 PDB 1DQA 205 kDa tetramer human EC 1.1.1.34 2Å
HMGCoA to mevalonate HMGCoA reductase is the first committed step on pathway toward steroid isoprenoids HMGCoA + 2NADPH + 2H+  mevalonate + 2NADP+ + CoASH Many drug-discovery projects involve inhibition of this enzyme 04/18/2019 Lipid Anabolism

63 Atorvastatin (lipitor)
Most prominent statin, i.e. inhibitor of HMGCoA reductase Until recently the biggest-selling prescription drug still on its original patent Other classes of statins exist Competitive inhibitor of enzyme: Km = 6 µM (low!); but KI = 5nM 04/18/2019 Lipid Anabolism

64 Mevalonate to isopentenyl diphosphate
Two successive ATP-dependent kinase steps convert mevalonate to mevalonate 5-diphosphate ATP-dependent decarboxylation yields isopentenyl diphosphate 04/18/2019 Lipid Anabolism

65 Significance of this compound
This is an isoprene-donating group involved in making non-steroidal isoprenoid compounds as well as steroids 04/18/2019 Lipid Anabolism

66 Mevalonate kinase Converts mevalonate to mevalonate 5-phosphate
Secondary control point in isoprenoid synthetic pathway PDB 2HFS 73 kDa dimer; monomer shown Leishmania major EC Å 04/18/2019 Lipid Anabolism

67 Human diseases and mevalonate kinase
Human diseases associated with abnormalities Mevalonic aciduria Hyperimmunoglobulinemia (Periodic fever syndrome) 04/18/2019 Lipid Anabolism

68 Isopentenyl diphosphate to squalene
Isomerized to dimethylallyl diphosphate + another IPDP: geranyl diphosphate (C10) Another condensation with IPDP (with the same enzyme) makes farnesyl diphosphate (C15) Two farnesyl diP fuse head-to-head to make squalene (C30, no heteroatoms) 04/18/2019 Lipid Anabolism

69 Geranyl diphosphate (C10)
04/18/2019 Lipid Anabolism

70 Farnesyl diphosphate (C15)
04/18/2019 Lipid Anabolism

71 Squalene Made via head-to-head synthesis from 2 molecules of farnesyl diphosphate; ER membrane enzyme Human squalene synthase EC 39kDa monomer PDB 3VJ8, 1.5Å Squalene: C30 04/18/2019 Lipid Anabolism

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