Histidine

http://chemistry.about.com/od/imagesclipartstructures/ig/Amino-Acid-Structures/Histidine.htm

General Features
Abbreviation: His or H
Chemical Formula:C₆H₉N₃O₂
Molar Mass: 155.15 g/mol
Histidine’s codons are CAU and CAC.  Histidine is an aromatic.  It contains six pi electrons; two from a nitrogen lone pair and four from double bonds.
Physiological Roles
Histidine has many roles.  It is part of catalytic triads.  In this, the basic nitrogen of histidine removed a proton from serine, threonine, or cysteine to create a nucleophile.  Histidine can also participate in proton shuttle.  Histidine does this by using the basic nitrogen to remove a proton to make a positively charged intermediate.  It then uses another molecule to take the proton from its acidic nitrogen. Histidine also plays a role in signal transduction in the form of histidine kinases (HK).  HKs act as cellular receptors for signaling molecules.  HKs typically have an extracellular domain, transmembrane domain, and intracellular domain.  The intracellular domain contain the enzymatic activity.  The intracellular domain also has a region that can bind to secondary effector molecules that further propagate the signal within the cell.  HKs are part of a two-component signal transducation mechanism.  Below is the mechanism of histidine kinase action.

http://en.wikipedia.org/wiki/File:HK_mechanism.png

HKs transfer a phosphate group from ATP to the histidine residue within the kinase and then to an aspartate residue on the receiver domain on a different protein.  For more information, see Two-Domain Reconstitution of a Functional Protein Histidine Kinase by Heiyoung Park, Soumitra K. Saha, and Masayori Inouye.

http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/AminoAcid/His1.html

http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/AminoAcid/His2.html

Synthesis
The synthesis of histidine is complex and its pathway intertwines with nucleic acid synthesis (purine specifically).  The pathway appears to be universal in all organisms that are able to synthesize histidine.  The first steps transform phosphoribosyl pyrophosphate (PRPP) into imadiazoleglycerol phosphate.  This begins with a condensation in which the N1 of the purine ring of ATP bonds to the C1 of ribose.  PRPP provides the five carbons of histidine.  The adenine ring of ATP provides the carbon and nitrogen of the imidazole ring.  Once the imadiazole ring is formed, glutamate donates the α-amino group.  The newly formed anime is oxidized to histidine in the last step.  For more information, see Synthesis of Histidine in Escherichia coli by John Westley and Joseph Ceithaml

Ribose 5-phosphate Family

Isoleucine

Add chttp://chemistry.about.com/od/factsstructures/ig/Chemical-Structures---I/D-Isoleucine.htmaption

General Features:

Abbreviated: Ile or I
Molecular formula: C₆H₁₃NO₂
pKa: 2.36 (carboxyl), 9.60 (amino)

Physiological Roles:
Isoleucine's codons are AUU, AUC and AUA and is a non polar amino acid.  It is classified as a hydrophobic amino acid because of the hydrocarbon side chain it possess.  Its side chain is chiral (like threonine) meaning it has four possible stereoisomers, L-Isoleucine is the most common form and the form found most often in nature.  As mentioned in the post on leucine, isoleucine is an isomer of leucine. 

In eukaryotes Isoleucine is an essential amino acid, it cannot be synthesised.  Foods that are high in this amino acid include eggs, soy protein, seaweed, turkey, chicken, lamb, cheese, and fish.

Isoleucine is a helpful amino acid in catabolic pathways.  It can be converted to acetyl-CoA or acetoacetyl-CoA and from there be feed into the TCA cycle,  It can also undergo transamination followed by oxidative decarboxylation and finally a series of oxidation reactions and be converted into propionyl-CoA.  Porpionyl-CoA is a precursor for Succinyl-CoA, an essential component of the citric acid cycle (Nelson et al).
In Bacillus subtilis a gene named bkdR was found to control the utilization of isoleucine and valine as sole nitrogen sources (Debarbouille et al 1999).

When isoleucine is converted to an α-Keto acid it uses a branched chain α-keto acid dehydrogenase complex.  When this enzyme is defective it results in a disease named maple syrup urine disease   

Synthesis

Synthesis of isoleucine

There are five main steps in the synthesis of isoleucine.

Threonine dyhydratases catalyzes the first step in isoleucine biosynthesis.  It will dehydrate threonine to create ammonia and 2-oxobutyrate.  It is at this step that feedback inhibition by isoleucine itself will occur

Asetolactate synthase (Acetohydroxyacid synthase) is the next step and will catalyses the condensation of  pyruvate and 2-oxobutyrate to yield acetohydroxybutyrate.  Thiamine pyrophosphate (TPP) is a cofactor in this reaction used to stabilize pyruvate. 

Acetohydroxyacid reductoisomerase will then reduce the acetohydroxybutyrate to produce 2,3-dihydroxy-3-methylvalerate.

From there dihydroxy-acid dehydratase will dehydrate the 2,3-dihydroxy-3-methylvalerate to form 2-oxo (keto)-3-methylvalerate

The final reaction is an aminotransferase from an amino acid donor to form isoleucine. 

Threonine

General Features:
Abbreviated: Thr or T
Chemical formula: C₄H₉NO₃

pKa: 2.63 (carboxyl), 10.43 (amino)

Physiological Roles:
Threonine is a polar amino acid and is one of the three proteinogenic ("protein-building") amino acids that contains an alcohol group. Its start codons are ACU and ACA. Due to its two chiral centers, it has four possible stereoisomers. L-threonine is the most common stereoisomer (the other L-isomer, L-allo-threonine, is relatively rare). It is the only common amino acid along with isoleucine that contains a chiral carbon in its side chain.

Because of its hydrophilic nature, threonine can be found in substantial concentrations at the outer regions of soluble proteins. Its easily removed hydrogen on the hydroxyl side chain makes it a common hydrogen donor in enzymes. The exact role of threonine's hydrogen donating in enzymes remains unclear, however.

Threonine is capable of posttranslational modification. In both eukaryotic and prokaryotic cells, threonine residues are able to undergo phosphorylation, which may have different effects depending on the particular protein. Threonine is the second most commonly phosphorylated amino acid residue, following serine. Interestingly, threonine-phosphorylated proteins are the easiest to purify using antibodies and are thus the most well characterized in terms of phosphorylation effects. Phosphorylated amino acids generally lose a hydroxyl group and gain a negatively charged phosphate. This negative charge may significantly alter the biochemical properties of the entire protein. The figure below gives a good visual as to how this negative charge might affect the amino acid (note that serine and tyrosine are shown as well):

Side chain modification (phosphorylation)

A specific example of the importance of threonine phosphorylation (carried out by enzymes called threonine kinases) is the autoregulatory effects of threonine kinases in the bacterial organism Bacilus anthracis (Bryant-Hudson et al., 2011). This study shows the first hints of inhibitory phosphorylation by a prokaryotic serine/threonine kinase (STK). Within the regulatory domain/activation loop of the STK, there are specific serine and threonine phosphorylation sites that may lead to either activation or inhibition. The enzyme itself may phosphorylate these sites; thus, the enzyme is autoregulatory.

Protons may be quickly abstracted from threonine using the basic nitrogen of histidine, making threonine nucleophilic. This may have implications in downstream pathways.

Synthesis and metabolism:
Threonine is an essential amino acid in humans, meaning we are unable to synthesize it naturally and must obtain it from food sources. Plants and microorganisms are able to synthesize threonine and utilize a pathway involving aspartic acid via alpha-aspartyl-semialdehyde and homoserine.

Synthesis of threonine

The enzymes featured in this pathway are:

1. aspartokinase (AK)

2. beta-aspartate semialdehyde dehydrogenase (B-ASD)

3. homoserine dehydrogenase (HSD)

4. homoserine kinase (HSK)

5. threonine synthase (TS)

With the coupling of ATP hydrolysis, aspartokinase (AK) catalyzes the phosphorylation of aspartate to form aspartyl-beta-phosphate. It has been shown that both plant and bacterial AK are bifunctional enzymes that may contain homoserine dehydrogenase activity (Weisemann and Matthews, 1993). B-ASD subsequently removes the phosphate group. These two reactions result in the removal of an oxygen and addition of a hydrogen through the usage of an activating phosphate. HSD catalyzes the first reaction which is specific to threonine, methionine, and isoleucine biosynthesis. 

HSK is an essential branch point between threonine and methionine biosynthesis; if homoserine acetyltransferase was present instead, methionine synthesis would follow. HSK catalyzes the formation of O-phosopho-L-homoserine via O-phosphorylation of homoserine. O-phosphorylation simply implies the addition of (ortho)phosphoric acid H₃PO_4.

TS catalyzes the final step of this biosynthetic pathway and involves a hydrolysis of the phosphate group added by HSK. TS shows functional domains that share similarities with SAM-dependent methyltransferases in plants (Thomazeau et al., 2001). Many of the enzymes in this pathway are great examples of how versatile enzymes can be. This makes the organism much more energy-efficient.

Below is a more broad picture to give you an idea how threonine biosynthesis is coupled to the TCA cycle. For the purpose of this section, feel free to only pay attention to the left portion of the diagram (keeping in mind the importance of the figure as a whole, of course).

Deng et al., 2011

Metabolism of threonine may occur by two pathways: conversion to pyruvate or conversion to alpha-ketobutyrate (which enters the pathway that leads to synthesis of succinyl-CoA). Threonine may also be converted to glycine via threonine aldolase:

Jander et al., 2009

Additional resources:

If you're really excited about threonine biosynthesis, you can visit The Enzyme Database for a very comprehensive look at each point of the pathway! Or if you're feeling particularly adventurous, take a look at this original publication by Kaplan and Flavin. Or if genetics is more your thing, check out this publication by Marchenko et al.

Although we mainly focus on amino acids as they pertain to prokaryotic organisms, this site may enlighten you to all the nutritional benefits of threonine in human diets. 

Methionine

Methionine

Abbreviated: Met or M

Molecular Formula: HO₂CCH(NH₂)CH₂CH₂SCH₃

pKa: 2.28(-COOH), 9.21 (α-NH₂)

Physiological roles:

• This amino acid is coded for by the codon AUG, which is the start codon for translation. In bacteria the derivative of Methionine, N-formylmethionine (fMet) is used to initiate translation. The formation of fMet is catalyzed by the enzyme methionyl-tRNA formyltransferase.
• fMet is highly important not only for the bacterial cell itself but also for the mitochondria and the chloroplasts.
• Interestingly there has been some research looking into the possibility of methionine restriction can extend life by alternative lengthening of telomeres genes. http://www.nature.com/onc/journal/v26/n32/full/1210260a.html 
• Methionine is an intermediate in the biosynthesis of cysteine, caritine, lecithin, phosphatidylcholine, taurine, and other phospholipids.

Synthesis:

Methionine biosynthesis

The enzymes involved in this synthesis are:

1. aspartokinase
2. β-aspartate semialdehyde dehydrogenase
3. homoserine dehydrogenase
4. homoserine O-transsuccinylase
5. cystathionine-γ-sythase
6. cystathionine-β-lyase
7. Methionine sythase

First, aspartic acid is converted via β-aspartyl-semialdehyde into homoserine, introducing the pair of contiguous methylene groups. Homoserine converts to O-succinyl homoserine, which then reacts with cysteine to produce cystathionine, which is cleaved to produce homocysteine. Subsequent methylation of the thiol group by folates affords methionine. Both cystathionine-γ-sythase and cystathionine-β-lyase require pyridoxyl-5'-phosphate as a cofactor, whereas homocysteine methyltransferase  requires vitamin B12 as a cofactor. (Lehninger, Albert L.; Nelson, David L.; Cox, Michael M. (2000), Principles of Biochemistry (3rd ed.), New York: W. H. Freeman, ISBN 1-57259-153-6).

To learn more about the initiation of protein synthesis with fMet in bacteria read the article, Initiation of Protein Synthesis in Bacteria LINK: http://mmbr.asm.org/content/69/1/101.short
 
 

Asparagine

Oxaloacetate Family: Asparagine (N)

General features

R group: -CH2-C(NH2)O

MW: 132.12 g mol^-1

pKa of R group: NA

Physiological roles

Glycosylation:

Personal annotation of figure from the abstract of Larkin, Imeriali (2011)

 http://pubs.acs.org/doi/abs/10.1021/bi200346n

Within the past decade it has been confirmed that eukaryotes are not the only domain that will link glycans to large proteins during their processing in the lumen of the ER. Gram negative species have been found to bind glycan (polysaccharide groups) to proteins in the periplasm. The polysaccharide is elongated on the cytoplasmic side of the cell membrane while anchored to the cell membrane via Und-PP. When finished, the Und-PP-polysaccharide is translocated to the outer leaflet to face the periplasm where it can be linked to finished protein via an asparagines residue on that protein.

 

http://pubs.acs.org/doi/abs/10.1021/bi200346n

 

This process is very similar to peptidoglycan and LPS synthesis.

Interesting to note, is that in the context of translation, tRNA^Asn is initially loaded with aspartate, and subsequently the carboxyl group is changed by an amidotransferase (this is also the case with tRNA^Gln). In this many bacteria lack an Asn tRNA synthetase but use a Asp tRNA synthetase that has amidotransferase activitiy.   This is thought to be a potentially mechanism for future antibiotics; this mode of interference with protein synthesis has already been implemented in cancer chemotherapy treatments. Just like with cancer chemotherapy, there is limitation to the selective toxicity of this method, because mitochondrial-directed translation also uses this modified Asn/Gln tRNA charging method. For more info, one of the situation is described in the in the introduction to this article: http://nar.oxfordjournals.org/content/early/2012/02/22/nar.gks167.full  It was also described in this review article:   doi: 10.1101/gad.1187404  Genes & Dev. 2004. 18: 731-738     Also, the characterization of the ribozyme that generates this ‘different’ Asn-tRNA can be read in this paper:  http://www.ncbi.nlm.nih.gov/pubmed/18241796

Synthesis

http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00134

Two enzymes (from independent genes) are known to synthesize asparagine in bacteria: AsnA , which  catalyzes the reaction referred to as “ammonia-dependent” and can only use ammonia as the nitrogen source to convert aspartic acid to asparagines, and AsnB, whose reaction is referred to as “glutamine-dependent” can use either ammonia or glutamine as the nitrogen donor (often glutamine). AsnB  has amidotransferase activity (meaning it transfers the transfer of the amide group of one amino acid to another.) The AsnA pathway is found only in prokaryotes while the AsnB pathway exists in eukaryotes as well as prokaryotes. Because of that fact, and the efficacy of cancer chemotherapeutics effective in the AsnB directed pathway, this enzyme/pathway is better studied than that of AsnA.

Ammonia-dependent (AsnA):

ATP + L-aspartate + NH₃ = AMP + diphosphate + L-asparagine

Glutamine-dependent (AsnB):

ATP + L-aspartate + L-glutamine + H₂O = AMP + diphosphate + L-asparagine + L-glutamate

Lysine

http://chemistry.about.com/od/imagesclipartstructures/ig/Amino-Acid-Structures/Lysine.htm

General Features
Abbreviation: Lys or K
Molecular Formula: HO₂(CCH(NH₂)(CH₂)₄NH₂

Lysine's codons are AAA and AAG.  It is a base.  The ε-amino group (a primary amine) can participate in hydrogen bonding.  The ε-amino acid can also serve as a general base in catalysis

Physiological Roles
Lysine has been shown to be essential in the chemotactic response of bacteria, including Escherichia coli and Salmonella typhimurium.  In chemotaxis, the activity of CheA, the histidine protein kinase, is controlled by sensory receptor proteins in the cytoplasmic membrane.  CheA phosphorylates CheY, the chemotaxis response regulator.  CheY interacts with the flagellar motor apparatus and the phosphorylation of CheY results in a tumbling response.  Aspartate has been shown to be the site of phosphorylation.  In close proximity to this site is a lysine residue.  This lysine residue is essential in producing the tumbling motion.  Regardless of the level of phosphorylation, removal of the lysine residue inhibits the tumbling motion.  It is believed that the lysine residue is required for an event after the phosphorylation.  An interaction between the ε-amino of lysine and the phosphoryl group at aspartate is required for the conformational change that leads to the activation of CheY.  More information is available in Roles of the Highly Conserved Aspartate and Lysine Residues in the Respone Regulator of Bacterial Chemotaxis by Gudrun S. Lukat et al.


Synthesis
The synthesis of lysine begins by converting oxaloacetate to aspartate.  Aspartate is then converted to L-aspartyl-4-phosphate.  This is done by aspartokinase and ATP is required.  L-aspartyl-4-phosphate is then converted to aspartate semialdehyde by β-Aspartate semialdehyde dehydrogenase. NADPH provides energy in this step.

The synthesis of lysine has been found to vary in different bacterial species.  A generalized pathway is present below.  Dihydrodipicolinate synthase adds pyruvate and two molecules of water are removed.  Cyclization then occurs forming 2,3-dihydrodipicolinate.  The product is then reduced by dihydrodipicolinate reducatase, consuming a NADPH molecule.  Tetrahydrodipicolinate N-acetyltransferase opens the ring.  Two molecules of water and one acyl-CoA (or succinyl-CoA) are used in this step.  The group added from CoA protects the amino group from attack during transamination by glutamate.

Succinyl diaminopimelate aminotransferase catalyzes the formation of N-succinyl-LL-2,6-diaminoheptanedionate.  Glutaric acid is used and an oxoacid is produced in this reaction.  An acyldiaminopimelate deacylase converts the product into LL-2,6-diaminoheptanedionate.  This is then converted into meso-2,6-diamino-heptanedionate by diaminopimelate epimerase.  Finally, diaminopimelate decarboxylase converts meso-2,6-diamino-heptanedionate into L-lysine.

http://en.wikipedia.org/wiki/File:Lysine_Biosynthesis.png

The synthesis of lysine has been found to vary in different bacterial species.  For more information on different synthesis pathways, please read A Functional Split Pathway for Lysine Synthesis in Corynebacterium glutamicum  Barbel Schrumpf et al.

Aspartate

Aspartate 

General Features

Abbreviated:  Asp or D

Molecular Formula: C₄H₇NO₄ 

pKa: 2.10 (caboxyl), 9.82 (amino), 3.86(side chain)

Physiological Roles

Aspartate, also called aspartic acid, is an α-amino acid.  Its codons are GAU and GAC.  It is among the twenty amino acids that is proteinigenic, a building block for proteins.  As told in the name it has acidic properties due to its side chain.  There are two forms of aspartic acid, L-aspartic acid being the far more common and the form that is proteinigenic. It is a nonessential amino acid meaning that humans have pathways of synthesis for it. 

Aspartic acid helps in the formation purines and pyrimidines which are key in DNA synthesis.  In eukaryotes it is also plays an important role in the urea cycle in the form of argininosuccinic acid.  One of the more interesting roles of aspartic acid in the human body is its role as a neurotransmittor.  D-Aspartic acid has been found in the central nervous system of both vertebrates (rats) and invertebrates (mollusks) (D’Abuello et.al).  High concentrations of D-Aspartate were found in synaptic vesicles of axon terminals.  When nerve endings with high D-aspartate are stimulated, signal transduction is triggered by increasing the levels of the secondary messenger cAMP. 

In bacteria aspartate plays an important role in chemotaxis.  The chemotactic responses of bacteria such as Escherichia coli and Salmonella typhimurium are mediated by phosphorylation of the CheY protein.  In the CheY protein there are two highly conserved residue of aspartate, Asp57, Asp13 (Lukat et al).  The actual site of CheY phosphorilation is Asp57. 

Synthesis

Aspartate biosynthesis

Aspartate biosynthesis is fairly straightforward.  Oxaloacetate is converted to aspartate using a transaminase.  The reaction can be revered so that aspartate can be converted back to oxaloacetate using an aspartate aminotransterase and ultimately end up in the citric acid cycle.