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22.2: Biosynthesis of Amino Acids

  • Page ID
    15179
  • In humans

    Nonessential amino acids:  Alanine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine

    Essential amino acids:  Arginine*, Histidine, Isoleucine, Leucine, Lysine, Methionine*, Phenylalanine*, Threonine, Tryptophan, Valine

    Three of the essential amino acids can be made in humans but need significant supplementation.  Arginine is depleted in processing through the urea cycle.  When cysteine is low, methionine is used to replace it so its levels fall.  If tyrosine is low, phenylalanine is used to replace it.

     

    summaryAASyntheis_TCA_Glycolysis.png

     

    Glycolytic Intermediates

     

    A.  From Glucose-6-Phosphate: His

    His

     

    His_Synthesis.png

     

     

     

    "The enzyme is involved in histidine biosynthesis, as well as purine nucleotide biosynthesis. The enzymes from archaea and bacteria are heterodimeric. A glutaminase component (cf. EC 3.5.1.2, glutaminase) produces an ammonia molecule that is transferred by a 25 A tunnel to a cyclase component, which adds it to the imidazole ring, leading to lysis of the molecule and cyclization of one of the products. The glutminase subunit is only active within the dimeric complex. In fungi and plants the two subunits are combined into a single polypeptide"  KEgg - https://www.genome.jp/dbget-bin/www_....3.2.10+R04558

    B. From 3-phosphoglycerate: Serine, Glycine and Cysteine

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    SerGlyCys_Synthesis.png

     

     

     

     

    dfdfee

    C.  From Phosphenol Pyruvate: The Aromatics - Trp, Phe and Tyr

     

    Scheme 1.

    The aromatics Phe, Tyr, Trp

    https://www.jbc.org/content/279/44/45618.long

     

    Shikimage_Synthesis_commontoAromaticAAsyn.png

     

     

    Second haf:  Choristmate → Trp

    ChoristmatentoTrpSyn.png

    anthranilate ketol-isomerase

    https://www.ebi.ac.uk/thornton-srv/m-csa/entry/328/

     

    https://www.ebi.ac.uk/thornton-srv/m-csa/entry/252/

     

     

    anthranilate synthase:  transfer of an amino group, (generated from glutamine) using a catalytic triad of with well-known mechanism consisting of Cys84, His175, and Glu177. In the second AIDC lyase part of the reaction a standard second-order elimination can be invoked to yield the double bond between C2 and C3 with a histidine (H306) as the base abstracting the C2 proton and pyruvate as the leaving group. Mg(II) and water provide an assisting acid group.  https://www.ebi.ac.uk/thornton-srv/m-csa/entry/314/  

     

    Chorismate to Phe and Tyr

    https://www.ebi.ac.uk/thornton-srv/m-csa/entry/485/

    ChoristmatentoPheTyrSyn.png

     

     

     

     

    D.  From Pyruvate: Ala, Val, Leu, Ile

    Ala can easily be synthesized from the alpha-keto acid pyruvate by a transamination reaction, so we will focus our attention on the others, the branched chain nonpolar amino acid Val, Leu, and Ile.

     

     

    Val_Synthesis.png

     

    TCA Intermediates

    E.  From alpha-ketogluatarate: Glu, Gln, Pro, Arg

    Since amino acid metabolism is so complex, it's important to constantly review past learning.  The image below from section 18.2 shows the relationship among Glu, Gln and keto acids.

     

    metabolismWP_GlnMet4.png

    As is evident from the figure, glutamic acid can be made directly through transamination of alpha-ketoglutarate by an ammonia donor, while glutamine can be made by the action of glutamine synthase on glutatic acid.  

    Arg is synthesized in the urea cycle as we have seen before.  It can be made from alpha-keto glutarate through the following sequential intermediates:  N-acetylglutamate, N-acetylglutamate-phosphate, N-acetylglutamate-semialdehyde, N-acetylornithine to N-acetylcitruline.  The is deacetylated to and enters the urea cycle.

    Proline:  

     

    ProSynthesis.png

    F.  From oxalacetate: Asp, Asn, Met, Thr, Lys

    OAA to Asp

    This is a a simple transamination

    Asp to Asn

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    Asp to Lys

     

    "Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes l-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilized by most bacteria, some archaea, some fungi, some algae, and plants (2829). The AAA pathway synthesizes l-lysine from α-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and α-aminoadipic acid is an intermediate.  This pathway is utilized by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea"  https://jb.asm.org/content/192/13/3304  

    Here present just the diaminopimelic acid DAP pathway.

     

    below:

    https://biocyc.org/gene?orgid=ECOLI&...PICSYN-MONOMER

    he reaction proceeds via a ping-pong bi-bi mechanism; pyruvate initially binds to the enzyme via a Schiff base to the ε-amino group of the active site Lys161 residue [Laber92]. This is followed by addition of L-aspartate semialdehyde and transimination leading to cyclization and dissociation of HTPA [Blickling97]. The kinetic mechanism was refined using initial velocity and dead-end inhibition studies at both high and low pH, confirming the ping-pong reaction mechanism of the enzyme [Karsten97]. Surprisingly, Lys161 is not absolutely essential for catalysis 

     

    real product of this enzyme being 4-hydroxy-2,3,4,5-tetrahydro-L,L-dipicolinic acid, it is still known in most publications as dihydropicolinate synthase (DHDPS).

    4-Hydroxy-tetrahydrodipicolinate synthase, historically called dihydrodipicolinate synthase (DHDPS, DapA) is the first enzyme unique to lysine biosynthesis, catalyzing the condensation of pyruvate and (S)-aspartate β-semialdehyde. This is thought to be the rate-limiting step in lysine biosynthesis after aspartate kinase III [Laber92]. The product of the reaction catalyzed by DapA was identified as (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate (HTPA) [Blickling97].

    LysSynthesis.png

    Asp to Thr

    dfxcxc

     

    "Threonine synthase (ThrS) catalyzes the final chemical reaction of l-threonine biosynthesis from its precursor, O-phospho-l-homoserine. As the phosphate ion generated in its former half reaction assists its latter reaction, ThrS is recognized as one of the best examples of product-assisted catalysis

    https://pubs.acs.org/doi/10.1021/acs...ed%20catalysis.

    ThrS processes the most complicated reaction of the PLP enzymes, and all seven types of the intermediate states known for PLP enzymes are formed during its catalytic cycle. As the result, there are many chances of side reactions taking place

    ThrSynthesis.png

     

    Asp to Met

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    DJFKDJFJDKJFKDJF

    MetSynthesis.png

     

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