Dihydrofolate Reductase

The enzyme Dihydrofolate reductase (DHFR) is found in the cytoplasmic region of bacteria. It catalyzes the last step in the biosynthetic pathway of tetrahydrofolic acid and is the target of the US FDA approved antibacterial drug trimethoprim, an example of a diaminopyrimidine class of antibiotic.

Function

The enzyme DHFR is responsible for NADPH-dependent reduction of 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate. Metabolites of tetrahydrofolate serve as cofactors for the synthesis of protein and DNA precursors that are essential for cell division and growth (Khavrutskii et al., 2007).

Figure 1. NADPH-dependent reduction of dihydrofolate to tetrahydrofolate catalyzed by DHFR. Image created using ChemDraw.
Figure 1. NADPH-dependent reduction of dihydrofolate to tetrahydrofolate catalyzed by DHFR. Image created using ChemDraw.

Although DHFR is present in all organisms, there are some differences between human and bacterial DHFR. For instance, the sequences of DHFR in humans and Escherichia coli are only 26% identical (Liu et al., 2013). Furthermore, bacterial DHFR is a smaller and more streamlined version than the one present in human cells. Because of the structural differences that exist between bacterial and human DHFR, it is seen as an attractive target for antimicrobial agents.

Structure

In E. coli, DHFR has 159 amino acids. It contains a single chain that folds into two domains. The refined structure, which was determined using X-ray crystallography, includes all 159 residues and is in complex with NADP+ and folate (Sawaya and Kraut, 1997). The DHFR enzyme in E. coli includes:

* The adenosine binding domain (residues 38-88, colored green)
* The loop domain, which is sometimes called the “major” domain (residues 1-37 and 89-159, colored blue)

Figure 2. Ribbon representation of DHFR in complex with NADP+ (grey) and folic acid (purple). The two domains of DHFR are colored green and blue (PDB ID: 1rx2, Sawaya and Kraut, 1997).
Figure 2. Ribbon representation of DHFR in complex with NADP+ (grey) and folic acid (purple). The two domains of DHFR are colored green and blue (PDB ID: 1rx2, Sawaya and Kraut, 1997).

The overall structure consists of eight central β-sheets and four flanking α-helices. The cleft of the active site divides the enzyme into its two domains. The adenosine binding domain is the smallest and serves as the binding site for the adenosine moiety of the cofactor. The loop domain consists of about 100 residues and contains three key loops which make up over half of this domain. The loops are termed Met20 (residues 9-24), F-G (residues 116-132), and G-H (residues 142-150). These loops are dynamic and allow the enzyme to assume different conformations during ligand binding and catalysis (Schnell et al., 2004).

Figure 3. Ribbon representation of DHFR with a focus on the Met20 loop (yellow), F-G loop (orange), and G-H loop (red) of the loop domain (PDB ID: 1rx2, Sawaya and Kraut, 1997).
Figure 3. Ribbon representation of DHFR with a focus on the Met20 loop (yellow), F-G loop (orange), and G-H loop (red) of the loop domain (PDB ID: 1rx2, Sawaya and Kraut, 1997).

There are three distinct conformational states of DHFR which are determined according to the location of the Met20 loop relative to the active site: closed, occluded, and open (Figure 4). The conformation of the Met20 loop is dependent on the presence of ligands in the cofactor and substrate binding sites during the catalytic cycle. The specific ligands discussed here include dihydrofolate (DHF) and tetrahydrofolate (THF), while cofactors include reducing agent Nicotinamide adenine dinucleotide phosphate (NADPH), and its oxidized form (NADP+).

Closed: In reactant-like states (e.g., DHFR:NADPH, DHFR:NADPH:DHF), the enzyme is in the closed conformation. As can be seen in Figure 5a, the Met20 loop stacks against the nicotinamide ring of NADPH which shields the active site from solvents and helps position the nicotinamide ring (Arora and Brooks, 2010). The closed conformation allows for the substrate and cofactor to be in close proximity, within the active site.

Occluded: In states where the product is bound (e.g., DHFR:NADP+:THF, DHFR:THF, DHFR:NADPH:THF), the enzyme assumes the occluded conformation. The Met20 loop sterically hinders the active site to prevent cofactor binding which is depicted in Figure 5b (Arora and Brooks, 2010). This prevents the nicotinamide ring from reentering the active site (Reddish et al., 2016). When the enzyme transitions between a closed and an occluded state, it cycles through the intermediate open conformation. The Met20 loop faces away from the reactants which results in a widening of the cofactor binding site (Sawaya and Kraut, 1997).

Open: Since open conformation is an intermediate between the occluded and closed conformation (Figure 6), one might expect that the open conformation is physically between the occluded and closed conformations. However, the Met20 loop in the open conformation extends outward past the occluded and closed conformation. This is because a transition between the occluded and closed states does not entail a simple rotation on two hinges. The conformational change is due to large rotations of main chain residues and torsion angles. Therefore, loop motions extend past the boundaries of the occluded and closed conformations (Sawya and Kraut, 1997).

Figure 4. Diagram depicting conformational changes in the Met20 loop through the catalytic cycle of DHFR. Adapted from Schnell et al., 2004.
Figure 4. Diagram depicting conformational changes in the Met20 loop through the catalytic cycle of DHFR. Adapted from Schnell et al., 2004.
Figure 5. (a) Ribbon representation of the closed conformation of DHFR bound by folate and NADP+ (PDB ID: 1rx2, Sawaya and Kraut, 1997). (b) Ribbon representation of the occluded conformation of DHFR bound by a THF analogue and NADP+. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHF and NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).
Figure 5. (a) Ribbon representation of the closed conformation of DHFR bound by folate and NADP+ (PDB ID: 1rx2, Sawaya and Kraut, 1997). (b) Ribbon representation of the occluded conformation of DHFR bound by a THF analogue and NADP+. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHF and NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).
Figure 6. Superpositions of the three conformations of the Met20 loop. The loop in the occluded conformation is colored purple (PDB ID: 1rx6, Sawaya and Kraut, 1997). The loop in the closed conformation is colored light pink (PDB ID: 1rx2, Sawaya and Kraut, 1997). The loop in the open conformation is colored dark pink (PDB ID: 1ra2, Sawaya and Kraut, 1997).
Figure 6. Superpositions of the three conformations of the Met20 loop. The loop in the occluded conformation is colored purple (PDB ID: 1rx6, Sawaya and Kraut, 1997). The loop in the closed conformation is colored light pink (PDB ID: 1rx2, Sawaya and Kraut, 1997). The loop in the open conformation is colored dark pink (PDB ID: 1ra2, Sawaya and Kraut, 1997).

In the occluded conformation, Met16 and Glu17 project into the active site to prevent the nicotinamide ring from accessing the substrate. This conformation is stabilized through hydrogen bonds between Asn23 of the Met20 loop and Ser148 of the G-H loop. These interactions can be seen below in Figure 7.

Figure 7. Ribbon representation of key residues in the occluded conformation of DHFR. The inset shows hydrogen bonds colored in cyan that stabilize this conformation. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHFand NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).
Figure 7. Ribbon representation of key residues in the occluded conformation of DHFR. The inset shows hydrogen bonds colored in cyan that stabilize this conformation. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHFand NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).

In the closed conformation, Met16 and Glu17 flip out of the active site which allows for nicotinamide binding near the substrate. Asn18 and Met20 surround the substrate and cofactor to shield it from solvents. The closed conformation is stabilized by hydrogen bonds between Gly15 and Glu17 of the Met20 loop and Asp122 of the F-G loop, as shown in Figure 8. The hydrogen bonds between Asn23 and Ser148 in the occluded conformation are lost (Schnell et al., 2004).

Figure 8. Ribbon representation of key residues in the closed conformation of DHFR. The inset shows hydrogen bonds colored in cyan that stabilize this conformation (PDB ID: 1rx2, Sawaya and Kraut, 1997).
Figure 8. Ribbon representation of key residues in the closed conformation of DHFR. The inset shows hydrogen bonds colored in cyan that stabilize this conformation (PDB ID: 1rx2, Sawaya and Kraut, 1997).

Active Site

The catalytic site is found in the cleft between the two domains, where substrates and potential inhibitors will bind. In the closed conformation, NADPH makes several direct contacts with the Met20 loop. The nicotinamide ring forms a hydrogen bond with Ile14, while other parts of the molecule make van der Waals contacts with the backbones of Asn18 and Ala19 and the side chain of Met20. The folate molecule is mainly stabilized through van der Waals interactions between its pABA ring and Leu28 and Ile50 (Sawaya and Kraut, 1997). The interactions that NADPH and folate make with DHFR can be seen in Figure 9.

Figure 9. Ribbon representation of the active site in the closed conformation of DHFR (PDB ID: 1rx2, Sawaya and Kraut, 1997).
Figure 9. Ribbon representation of the active site in the closed conformation of DHFR (PDB ID: 1rx2, Sawaya and Kraut, 1997).

In contrast to the closed conformation, the occluded conformation inhibits NADPH binding through a 180° rotation of Ile14 into the nicotinamide binding pocket. This allows Met16 to form van der Waals contacts with Thr46 and Ser49. These interactions prevent NADPH from binding to folate and cause the nicotinamide ring to shift away from folate. The DHFR contacts with folate are mostly preserved in the occluded conformation. These interactions are shown in Figure 10.

Figure 10. Ribbon representation of the active site in the occluded conformation of DHFR. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHF and NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).
Figure 10. Ribbon representation of the active site in the occluded conformation of DHFR. The missing coordinates of NADP+ were added from the complex of DHFR with ddTHF and NADP+ (PDB IDs: 1rx6 and 1rc4, Sawaya and Kraut, 1997).

Pharmacological Implications

Bacteria are dependent on a functional DHFR enzyme to survive because it catalyzes the last step of the folic acid biosynthesis pathway (Fernandez-Villa et al., 2019). If DHFR is inhibited, bacteria would no longer be able to produce folic acid, which in turn, which would lead to bacterial cell death. Therefore, this enzyme remains an attractive target for novel antibacterial agents.

Specificity in Targeting

DHFR is one of the most targeted enzymes in medicine. Several compounds have been discovered that inhibit DHFR and are used to treat various types of cancers, autoimmune diseases, and protozoal infections. For example, methotrexate is an anticancer agent, also used to treat rheumatoid arthritis and psoriasis. It binds to eukaryotic DHFR with a high affinity, reducing the amount of folate required for DNA and RNA synthesis which leads to cell death (Raimondi et al., 2019). Other drugs that target DHFR are pyrimethamine and proguanil. These drugs competitively inhibit DHFR and are used to treat malaria infections (Raimondi et al., 2019).

References

Arora, K., Brooks, C. L. (2009). Functionally Important Conformations of the Met20 loop in Dihydrofolate Reductase are Populated by Rapid Thermal Fluctuations. Journal of the American Chemical Society, 131(15), 5642–5647. https://doi.org/10.1021/ja9000135

Fernández-Villa, D., Aguilar, M. R., Rojo, L. (2019). Folic Acid Antagonists: Antimicrobial and Immunomodulating Mechanisms and Applications. International Journal of Molecular Sciences, 20(20), 4996. https://doi.org/10.3390/ijms20204996

Khavrutskii, I. V., Price, D. J., Lee, J., Brooks, C. L. (2007). Conformational Change of the Methionine 20 loop of Escherichia coli Dihydrofolate Reductase Modulates pKa of the Bound Dihydrofolate. Protein Science: A Publication of the Protein Society, 16(6), 1087–1100. https://doi.org/10.1110/ps.062724307

Liu, C. T., Hanoian, P., French, J. B., Pringle, T. H., Hammes-Schiffer, S., Benkovic, S. J. (2013). Functional Significance of Evolving Protein Sequence in Dihydrofolate Reductase from Bacteria to Humans. Proceedings of the National Academy of Sciences of the United States of America, 110(25), 10159–10164. https://doi.org/10.1073/pnas.1307130110

Raimondi, M. V., Randazzo, O., La Franca, M., Barone, G., Vignoni, E., Rossi, D., Collina, S. (2019). DHFR Inhibitors: Reading the Past for Discovering Novel Anticancer Agents. Molecules (Basel, Switzerland), 24(6), 1140. https://doi.org/10.3390/molecules24061140

Reddish, M. J., Vaughn, M. B., Fu, R., Dyer, R. B. (2016). Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase. Biochemistry, 55(10), 1485–1493. https://doi.org/10.1021/acs.biochem.5b01364

Sawaya, M., Kraut, J. (1997). Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence. Biochemistry, 36(3), 586-603. https://doi.org/10.1021/bi962337c PDB IDs: 1ra2, 1rc4, 1rx2, 1rx6

Schnell, J., Dyson, H., Wright, P. (2004). Structure, Dynamics, and Catalytic Function of Dihydrofolate Reductase. Annual Review Of Biophysics And Biomolecular Structure, 33(1), 119-140. https://doi.org/10.1146/annurev.biophys.33.110502.133613

March 2025, Steven Arnold ; Reviewed by Dr. Christina Bourne
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/folate-synth/DHR