Key biosynthetic enzymes are regulated by their ultimate products through allosteric motions.
Cells often use assembly lines to create essential molecules like amino acids and nucleotides. An ordered pathway of enzymes work together, each making a specific chemical change to construct complex molecules from available starting materials. These assembly lines are usually carefully regulated, so that molecules are only made when they are needed. Often, this regulation occurs without a lot of administrative overhead—typically, the first enzyme in line will sense the current amount of the final product, and if there is enough, it shuts itself down, halting the whole assembly line. This has been termed “feedback inhibition,” and study of the enzyme aspartate transcarbamylase helped reveal how it’s done.
Aspartate transcarbamylase (ATCase) performs an early step in the production of pyrimidine rings, which are used to build nucleotides in DNA and RNA. Early studies found that when the levels of CTP (a nucleotide with a pyrimidine ring) get too high, the enzyme shuts down. Based on biochemical data, researchers proposed a model with two states: a “tense” T state that is inactive, and a “relaxed” R state that can perform the reaction. The structure of ATCase revealed how the level of nucleotides is sensed: in the middle, six catalytic chains perform the chemical reaction, and around the outside, three pairs of regulatory chains change the shape of the complex when they bind to CTP. The structure shown here (PDB entry 5at1
) is in the T state, with CTP bound in the regulatory sites. The six catalytic chains are also cooperative: as with the cooperativity of the four chains of hemoglobin
, binding of starting materials to a few active sites stabilizes the R state, making the whole complex more active.
Choosing the Control Point
Regulated enzymes usually perform the first step that is unique to a pathway. The synthesis of pyrimidines starts one step earlier than ATCase, when the enzyme carbamoyl-phosphate synthase (CPSase) creates carbamoyl phosphate from several common cellular building blocks. However, this carbamoyl phosphate is also used to make the amino acid arginine. Bacteria only make one form of CPSase, so it’s not the best enzyme to regulate, so pyrimidine synthesis is regulated by the second enzyme in the pathway, ATCase, which is only used to build pyrimidines. Our cells, however, have two different CPSases, one for pyrimidine synthesis and one involved in arginine synthesis. So in our cells, CPSase is the enzyme that regulates the synthesis of pyrimidines.
Three functional domains in CAD have been studied separately by x-ray crystallography by cutting the protein into pieces. In the intact protein, they are connected by flexible linkers, and come together to form a huge hexameric complex.Download high quality TIFF image
Our Pyrimidine Factory
In animal cells, ATCase is part of a large multifunctional protein, called “CAD”. Three steps of pyrimidine synthesis are performed by this huge complex. Two enzymes in glutamine-dependent carbamoyl-phosphate synthase (GLNase and CPSase) together create carbamoyl phosphate, ATCase connects it to aspartate, and dihydroorotase (DHOase) closes it into a ring that will be become the pyrimidine base (PDB entries 5dou
). The CPSase shown here is the one involved in arginine synthesis, which is similar to the CAD CPSase. Bacteria also have all of these enzymes, but they are typically made as individual proteins that perform their tasks separately. Notice that the human ATCase portion includes only catalytic subunits, without the regulatory subunits found in the bacterial enzyme complex.
Exploring the Structure
Dozens of structures of ATCase have been determined, capturing the enzyme in both the T and R states, and with a variety of substrates and inhibitors. Two are shown here, showing the amazing allosteric motion that occurs when the enzyme is activated. The T state (PDB entry 5at1) has CTP bound and the R state (PDB entry 8atc) has an inhibitor bound in the active site that looks much like the substrates. To explore these two structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- Many variations on ATCase and the other enzymes of pyrimidine synthesis have been observed in different organisms. For instance, take a look at PDB entry 3d6n for an example of a complex that includes both ATCase and DHOase.
- Many other enzyme pathways are controlled by this type of allosteric regulation. For instance, take a look at phosphofructokinase, which controls breakdown of sugar through glycolysis.
- M Moreno-Morcillo, A Grande-Garcia, A Ruiz-Ramos, F del Cano-Ochoa, J. Boskovic & S Ramon-Maiques (2017) Structural insight into the core of CAD, the multifunctional protein leading de novo pyrimidine biosynthesis. Structure 25, 912-923.
- 5g1n: A Ruiz-Ramos, A Velazquez-Campoy, A Grande-Garcia, M Moreno-Morcillo & S Ramon-Maiques (2016) Structure and functional characterization of human aspartate transcarbamylase, the target of the anti-tumoral drug PALA. Structure 24, 1081-1094.
- 5dou: S de Cima, LM Polo, C Diez-Fernandez, AI Martinez, J Cervera, I Fita & V Rubio (2015) Structure of human carbamoyl phosphate synthase: deciphering the on/off switch of human ureagenesis. Scientific Reports 5, 16950.
- 4c6i: A Grande-Garcia, N Lallous, C Diaz-Tejada & S Ramon-Maiques (2014) Structure, functional characterization and evolution of the dihydroorotase domain of human CAD. Structure 22, 185-198.
- WN Lipscomb & ER Kantrowitz (2011) Structure and mechanisms of Escherichia coli aspartate transcarbamylase. Accounts of Chemical Research 45, 444-453.
- 5at1: RC Stevens, JE Gouaux & WN Lipscomb (1990) Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-A resolution. Biochemistry 29, 7691-7701.
- 8atc: HM Ke, WN Lipscomb, YJ Cho & RB Honzatko (1988) Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. Journal of Molecular Biology 204, 725-747.
November 2017, David Goodsell