Serine hydroxymethyltransferase: Difference between revisions
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Serine Hydroxymethyltransferase exists in different forms. In Bacillus Stearthermophilus, SHMT exists as a dimer with two monomeric folds comprised of two separate domains. The enzyme monomer fold is comprised of the C-terminal domain and the N-Terminal Domain. The C-terminal domain folds into an αβ sandwich. The N-terminal domain is comprised of two further sub-domains. The first N-terminal sub-domain is a smaller domain composed of only 3 α-helices and 1 β-strand. The second N-terminal subdomain is the PLP binding domain. This sub-domain folds into an αβα structure that has a seven-stranded mixed β sheet surrounded by α-helices on both sides, hence αβα. | Serine Hydroxymethyltransferase exists in different forms. In Bacillus Stearthermophilus, SHMT exists as a dimer with two monomeric folds comprised of two separate domains. The enzyme monomer fold is comprised of the C-terminal domain and the N-Terminal Domain. The C-terminal domain folds into an αβ sandwich. The N-terminal domain is comprised of two further sub-domains. The first N-terminal sub-domain is a smaller domain composed of only 3 α-helices and 1 β-strand. The second N-terminal subdomain is the PLP binding domain. This sub-domain folds into an αβα structure that has a seven-stranded mixed β sheet surrounded by α-helices on both sides, hence αβα. | ||
[[Image:SubstrateBound.png|thumb|right|200px| SHMT residue interactions with PLP ]] | |||
The figure on the right | ===SHMT and PLP=== | ||
The figure on the right shows the PLP binding interactions with specific residues on SHMT. The PLP molecule binds to different residues based upon its orientation in the SHMT PLP binding pocket. Residues G94, H225, and A95 all interact with the phosphate group on PLP. Both G94 and A95 utilize hydrogen bonding between the amide hydrogen and and the oxygen on the phosphate group. In this case, these two residues are proton donors. H225 is an proton acceptor and utilizes the double bonded nitrogen on the Histidine ring to accept a proton from the only hydroxyl group on the phosphate portion of PLP. Residues S172, H200, K226, and D197 all hydrogen bond with the aromatic portion of PLP. S172, H200, and K226 all interact with the hydroxyl group on the aromatic portion of PLP. S172 is a proton donor, H200 is a proton donor, but K226 is a proton acceptor. A197 interacts with the nitrogen within the aromatic ring of PLP. A197 is the proton donor in this case. All of these residues interacting with PLP are polar. PLP has many polar entities including the phosphate, the hydroxyl group on the aromatic ring, and the nitrogen embedded within the aromatic ring. It is no surprise that PLP binds within a polar binding pocket in SHMT. The polar-polar interactions help stabilize the ligand within the binding pocket. | |||
[[Image: | [[Image:PLP_interactions.png|thumb|left|200px| SHMT residue interactions with serine substrate ]] | ||
===SHMT and Serine=== | |||
The figure on the left represents the substrate binding interactions with specific residues of the SHMT enzyme. T342 and N116 are very important residues for substrate binding within PLP. Once again the polar residues of SHMT bind to the polar serine substrate. A key factor for both the PLP and substrate binding is the specific hydrogen donating/accepting by the respective parts. One possible hypothesis to inhibition of SHMT comes from the differences in hydrogen bonding between substrate and inhibitor. In the substrates case, the serine substrate is primarily proton donating. In the case of inhibition through the use of antifolates, there are more hydrogen accepting atoms than hydrogen donating atoms. In fact, the binding portion of tetrahydrofolate (substrate) compared to methotrexate (inhibitor) makes it clear. THF substrate contains three proton donating atoms within the binding portion while methotrexate contains three proton accepting atoms within the binding portion. As we know, hydrogen bonding stabilizes the secondary structure of a protein. When methotrexate is introduced, hydrogen bonding shifts and destabilizes the protein. | |||
{{Clear}} | {{Clear}} | ||
=Mechanism of Action= | =Mechanism of Action= | ||
The most common accepted mechanism of action is through a process of modified retro-aldol cleavage. In this case, the mechanism starts with the serine/PLP-enzyme complex. The base represented by 'B' attacks the hydrogen of the ethyl alcohol functional group. The resonance allows the process of tautomerization to occur. This end results of tautomerization results in the formation of a formaldehyde, and acidic 'H-A' compound, and an imine attached to the serine-PLP complex. The double bond of the imine then reacts with the acidic 'H-A' compound. Resonance then allows the new complex to form the separated glycine and PLP-enzyme. | The most common accepted mechanism of action is through a process of modified retro-aldol cleavage. In this case, the mechanism starts with the serine/PLP-enzyme complex. The base represented by 'B' attacks the hydrogen of the ethyl alcohol functional group. The resonance allows the process of tautomerization to occur. This end results of tautomerization results in the formation of a formaldehyde, and acidic 'H-A' compound, and an imine attached to the serine-PLP complex. The double bond of the imine then reacts with the acidic 'H-A' compound. Resonance then allows the new complex to form the separated glycine and PLP-enzyme. | ||