Question

Perturbed \(\mathbf{p} \boldsymbol{K}_{\mathrm{a}}\) Values in Enzyme Active Sites Alanine racemase is a bacterial enzyme that converts \(\mathrm{L}\)-alanine to \(\mathrm{D}\) alanine, which is needed in small amounts to synthesize the bacterial cell wall. The active site of alanine racemase includes a Tyr residue with a p \(K_{\mathrm{a}}\) value of \(7.2\). The \(\mathrm{p} K_{\mathrm{a}}\) of free tyrosine is 10 . The altered \(\mathrm{p} K_{\mathrm{a}}\) of this residue is due largely to the presence of a nearby charged amino acid residue. Which amino acid(s) could lower the \(\mathrm{p} K_{\mathrm{a}}\) of the neighboring Tyr residue? Explain your reasoning.

Short answer

Arginine, lysine, or histidine could lower the pKa of tyrosine by stabilizing its deprotonated form through positive charges.

Step-by-step solution

Understand pKa Concept

The pKa value is a measure of the acidity of a substance. A lower pKa indicates a stronger acid capable of donating a proton more readily. When we compare pKa values of a substance in different environments, such as free form and within an enzyme active site, it indicates the effect of the local environment on the acidity of that residue.

Identify Modification of pKa

In the given question, tyrosine within the enzyme active site has a pKa of 7.2 compared to 10 when free. The decrease in pKa suggests tyrosine becomes a stronger acid, likely due to the influence of nearby charged amino acid residues.

Role of Nearby Charged Amino Acids

Charged amino acids can alter the pKa of nearby residues by stabilizing the charged form of the residue. Specifically, a positive charge near tyrosine would attract its deprotonated form, lowering the pKa by making it easier to donate a proton.

Identify Possible Amino Acids

To stabilize the negatively charged (deprotonated) form of tyrosine, nearby positively charged residues would be necessary. The amino acids with positive charges at physiological pH are lysine (Lys), arginine (Arg), and histidine (His). These amino acids could potentially lower the pKa of tyrosine in the active site.

Key concepts

Alanine Racemase

Alanine racemase is an enzyme that plays a crucial role in the conversion between the two forms of alanine: L-alanine and D-alanine. This process is essential for bacterial survival as D-alanine is a key component in the synthesis of the bacterial cell wall. Without D-alanine, bacteria cannot maintain a structurally sound cell wall, which can lead to their demise.
Alanine racemase contains an active site where this conversion takes place. The environment within the active site is specifically tailored to facilitate the racemization reaction. It achieves this by ensuring optimal conditions for breaking and reforming chemical bonds. The role of different residues, such as tyrosine, within the active site, is crucial as they can influence the reaction's pH sensitivity by altering the pKa.

• It converts L-alanine to D-alanine.
• D-alanine is important for bacterial cell walls.
• The active site environment is vital for the enzyme's function.

pKa Values

The concept of pKa values is fundamental in understanding the acidity of molecular components within biological systems. A pKa value quantifies how easily a substance can donate a proton. Therefore, the lower the pKa, the more acidic the molecule is, meaning it can donate its proton more readily. In the context of enzymes, changes in pKa can reflect interactions with surrounding residues. Such changes can dramatically influence enzyme activity and function.
Within enzyme active sites, the pKa of residues like tyrosine can be altered significantly compared to their free counterparts. In our example, tyrosine's pKa drops from 10 in its free form to 7.2 within the active site. This shift towards being a stronger acid indicates a change in its local environment, often due to adjacent charged residues.

• pKa measures how easily a substance donates a proton.
• Lower pKa values indicate stronger acidic properties.
• Changes in pKa values provide insights into the molecular environment.

Charged Amino Acids

Charged amino acids are pivotal components in influencing the pKa values of nearby residues in enzyme active sites. Their role is to stabilize charged forms of neighboring molecules, which can either raise or lower the pKa value depending on the charge interaction. Positive charges, for example, can attract the negative form of a deprotonated residue, resulting in a lower pKa by making it energetically favorable for the residue to release a proton.
In the active site of alanine racemase, positively charged residues like lysine (Lys), arginine (Arg), and histidine (His) are candidates for this interaction. These residues, each possessing a positive charge at physiological pH, can stabilize the negatively charged form of tyrosine once it donates a proton. By stabilizing this state, they effectively make it easier for tyrosine to lose its proton, lowering its pKa.

• Charged amino acids can stabilize charged molecules.
• Positive charges make proton donation by nearby residues easier.
• Lysine, arginine, and histidine are potential influencers in alanine racemase.