Amino acid metabolism, concluded Andy Howard Introductory Biochemistry 24 April 2008

Amino acid metabolism, concluded

Andy HowardIntroductory Biochemistry

24 April 2008

24 April 2008Amino Acid metabolism p. 2 of 44

What we’ll cover Amino acid

metabolism Non-essential amino

acids Branched-chain Aromatics Histidine

Amino acids as metabolites Glucogenic amino

acids Ketogenic amino

acids Serine biproducts Glycine biproducts


Essential and non-essential amino acids An amino acid is defined as essential if it

must be obtained within the diet In general the essential amino acids are

the ones that have complicated and highly ATP-dependent biosynthetic pathways

Of course, it depends on the organism


The human list (cf. box 17.3)

AA moles ATPessen- tial?

Asp 21 noAsn 22-24 noLys 50-51 yesMet 44 yesThr 31 yesAla 20 noVal 39 yesLeu 47 yesIle 55 yesGlu 30 noGln 31 no

AA moles ATP essen-tial?

Arg 44 noPro 39 noSer 18 noGly 12 noCys 19 noPhe 65 yesTyr 62 no*Trp 78 yesHis 42 yes


Examples of transaminasesReactants Products TransaminaseKeto acid amino acid keto acid amino acidPyruvate glutamate -k-glutarate alanine pyruvatePyruvate aspartate oxaloacetate alanine pyruvateOxaloacetate glutamate -k-glutarate aspartate aspartate3-P-OH-pyr glutamate -k-glutarate P-ser phosphoserine3-OH-phenyl- glutamate -k-glutarate tyrosine tyrosine

pyruvateGlu-g- (glu) (-k-g) ornithine ornithine

semialdehydeN-acyl- glutamate -k-glutarate N-acyl- 2.3.1.89

2-amino- 2-6,diamino-6-oxopimelate pimelate


Marching through the list of twenty amino acids

Amino acids we’ve already covered Acids and amides:

glu, gln, asp, asn Simple:

ala, ser, gly New but non-

essential arg, pro cys

Essential but straightforward lys, met, thr val, leu, ile

Essential & Ugly phe, tyr, trp his


Arginine and proline Two routes: Glutamate to glutamate semialdehyde

that cyclizes to 1-pyrroline 5-carboxylateand thence to proline

Glutamate semialdehyde can also be converted to ornithine and thence to arg

Alternative: glutamate acetylated to N-acetyl-glutamate-5-semialdehyde and thence to ornithine

Glutamate semialdehyde

ornithine


Glutamate to P5C

Single enzyme can interconvert glutamate and 1-pyrroline carboxylate:1-pyrroline-5-carboxylate dehydrogenase

3-layer sandwich protein

PDB 2BJA170 kDa trimermonomer shownThermus thermophilus


Pyrroline-5-carboxylate to proline

Pyrroline-5-carboxylate reduced to proline

Large, NAD(P)-dependent enzyme

Pyrroline-5-carboxylate reductasePDB 2IZZ354 kDa decamerpentamer shownHuman


Glutamate to Glu semialdehyde

Glu is -phosphorylated:glu + ATP glu-5-P + ADP (2.7.2.11)

Glu-5-P is reduced and dephosphorylated:glu-5-P + NADPH + H+ glu-5-semialdehyde + NADP+

-glutamyl phosphate reductasePDB 1O2047 kDa monomerThermatoga maritima

Glu-5-P


Glu semialdehyde to ornithine

This is just another transamination, catalyzed by ornithine aminotransferase:glu-5-semialdehyde + glu/asp ornithine + -keto-glutarate / oxaloacetate

Typical PLP-dependent reaction

PDB 2OAT193 kDa tetramerhuman

ornithine


Ornithine to citrulline

Ornithine condenses with carbamoyl phosphate to form citrulline with the help of ornithine transcarbamoylase

Carbamoyl phosphate

PDB 1DUV110 kDa trimerE.coil

citrulline


Citrulline to arginosuccinate

Citrulline condenses with aspartate using ATP hydrolysis to drive it forward to L-arginosuccinate:citrulline + aspartate + ATP L-arginosuccinate + AMP + PPi

Arginosuccinate synthase200 kDa tetramermonomer shown


Arginosuccinate to arginine

Fumarate extracted,leaving arginine

Arginosuccinate lyase is also -crystallin, one of the moonlighting proteins: it’s a component of eye lenses

PDB 1TJ7100 kDa dimer(really!)E.coli

fumarate


Why all that detail?

These reactions form 75% of the urea cycle, which is an important path for amino acid and nucleic acid degradation.

So we’ll need this later.


Cysteine synthesis in plants and

bacteria serine + Acetyl CoA

O-acetylserine + HSCoA O-acetylserine + S2- + H+

cysteine + acetate Ser acetyltransferase is

inhibited by cysteine

Serine acetyltransferasePDB 1SSQ176 kDa hexamerdimer shownHaemophilus

O-acetylserine


Animal pathway to cys

Ser + homocysteine (from met) fuse to form cystathionine + H2O

Cystathionine + H2O NH4

+ + cysteine + -ketobutyrate

Cystathionine -lyasePDB 1N8P173 kDa tetrameryeast

cystathionine


Lys, met, thr asp gets phosphorylated and

becomes a source for all of these: Asp + ATP

-aspartyl phosphate + ADPvia aspartate kinase

-asp P + NADPH + H+ -> Pi + aspartate -semialdehyde +NADP+

This heads to lys or to homoserine Homoserine converts in a few steps

to met or thr

Aspartate kinase112 kDaPDB 2CDQdimerArabidopsis


Asp -semialdehyde to homoserine

-aldehyde reduced to sec-alcohol, which is homoserine

Homo is generally a prefix meaning containing an extra methylene group

This is precursor to homocysteine methionine

It also leads to threoninehomoserine


Homoserine to threonine

Homoserine phosphorylated with ATP as phosphate donor

Phosphohomoserine dephosporylated with movement of -OH from one carbon to another: threonine results

Phospho-homoserine

threonine


Homoserine to methionine

Three reactions convert homoserine to homocysteine

5-methyltetrahydrofolate serves as a methyl donor to convert homocysteine to methionine via methionine synthase

This enzyme exists in humans but its activity is low and [homocysteine] is low;

So methionine is essential in humans

homocysteine


Specifics for lysine

Aspartyl semialdehyde condenses with pyruvate to form 2-3-dihydropicolinate

Reduced again to 2,3,4,5-tetrahydropicolinate Acylated (via AcylCoA) to N-acyl-2-amino-6-

oxopimelate Transaminated to N-acyl-2,6-diaminopimelate Deacylated to L,L-N-acyl-2,6-diaminopimelate Epimerase converts that to meso form That’s decarboxylated to lysine

2,3-dihydro-picolinate


The human list (cf. box 17.3)

AA moles ATPessen- tial?

Asp 21 noAsn 22-24 noLys 50-51 yesMet 44 yesThr 31 yesAla 20 noVal 39 yesLeu 47 yesIle 55 yesGlu 30 noGln 31 no

AA moles ATP essen-tial?

Arg 44 noPro 39 noSer 18 noGly 12 noCys 19 noPhe 65 yesTyr 62 no*Trp 78 yesHis 42 yes


Branched-chain aliphatics:isoleucine and valine

Derived from pyruvate or -ketobutyrate

2 pyruvate -ketoisovalerate + CO2

pyr + -ketobutyrate -keto--methylvalerate + CO2

These products are transaminated to ile and val

-ketobutyrate

-keto-methylvalerate


Leucine

Also derived from -ketoisovalerate; An extra methylene is inserted between

the polar end and the isopropyl group Final reaction is another transamination


Aromatics: phe and tyr

Common pathways for phe,tyr,trp via shikimate and chorismate

For phe, tyr: chorismate converted to prephenate

Prephenate can be aromatized with or without a 4-OH group to lead to phe,tyr

chorismate

shikimate


Reaction specifics Prephenate is oxidized

and dehydroxylated in two steps to phenylpyruvate

Or it is oxidized to 4-OH-phenylpyruvate

Transaminations of those -ketoacids yield the final amino acids

prephenate

4-hydroxy-phenyl-pyruvate


Chorismate mutase

Isomerase, converts chorismate to prephenate

In E.coli: 2 versions depending on which path the product is heading to

Active sites are similar in all organisms but architecture is very different

Catalytic triad similar to serine proteases

PDB 1DBF42 kDa trimerB.subtilis


Path to tryptophan:anthranilate synthase

Chorismate reacts with glutamine and is aromatized to anthranilate:chorismate + gln anthranilate + pyruvate + glutamate

anthranilate

PDB 1I1Q157 kDaheterotetramerheterodimershownSalmonella


Anthranilate to indole

Four-step pathway: phosphoribosyl pyrophosphate (PRPP)

contributes a phosphoribosyl group Sugar ring opens and rearranges Result is decarboxylated and forms a second

ring to form indole 3-glycerinphosphate Glyceraldehyde-3-P is released to leave

indole


Tryptophan synthase

Indole + ser tryptophan + H2O

PLP-dependent enzyme, but different in how it uses PLP from the transaminases

PDB 2CLF146 kDaheterotetramer;heterodimershownSalmonella


Genetic control of aromatic aa synthesis

In E.coli and other bacteria, a single operon controls several chorismate-related genes


Histidine (fig. 17.22)

Start with PRPP and ATP: form phosphoribosyl ATP

3 reactions involving glutamine as nitrogen donor for ring lead to imidazole glycerol phosphate

That gets modified and transaminated t make histidine


What do we do with amino acids?

Obviously a lot of them serve as building-blocks for protein and peptide synthesis via ribosomal mechanisms

Also serve as metabolites, getting converted to other compounds or getting oxidized as fuel


Gluogenic and ketogenic amino acids

Degradation of many amino acids lead to TCA cycle intermediates or pyruvate therefore these can be built back up to glucose; these are called glucogenic

Degradation of others leads to acetyl CoA and related compounds these cannot be built back up to glucose except

via the glyoxalate shuttle these are called ketogenic


Serine-based metabolites

Serine is a building block for sphinganine and therefore for sphingolipids

Serine also leads to phosphatidylserine, which is important by itself and can be metabolized to phosphatidylethanolamine and phosphatidylcholine


Glycine-based metabolites Glycine is a source for purines,

glyoxylate, creatine phosphate, and (with the help of succinyl CoA) porphobilinogen, whence we get porphyrins, and from those we get chlorophyll, heme, and cobalamin

porphobilinogen


We’ll continue amino acids next time… But first, a sneak preview of our coverage

of nucleic acid chemistry, which we’ll do on Tuesday!


Pyrimidines Single-ring nucleic acid bases 6-atom ring; always two nitrogens in the ring,

meta to one another Based on pyrimidine, although pyrimidine itself

is not a biologically important molecule Variations depend on oxygens and nitrogens

attached to ring carbons Tautomerization possible Note line of symmetry in pyrimidine structure

N

N

pyrimidine

1

2

3

4

5

6

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Amino acid metabolism, concluded Andy Howard Introductory Biochemistry 24 April 2008