Shigella Dysenteriae Serotype 2

Background

In this display, the red portion is subunit A, and the yellow portion is subunit B.

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Structure

Subunit A is the same as chain A in the pdb file 1R4P. The A-subunit consists of two parts, A1 and A2, connected by a disulfide bond (green) which is broken in the cytoplasm. A2 acts as the anchor between the A1 and B subunits. After the disulfide bond is broken, A1 travels to the ribosome to target protein synthesis. Therefore, A1 is known as the toxic portion because its amino acids form N-glycosidase which is responsible for cleaving a single adenine base off of 28S from rRNA. As a result, elongation factor binding is inhibited and protein synthesis is stopped. In the end, cells die because they cannot function without protein synthesis.

As the disulfide bond (green) breaks, A1 and A2 form (A1 is black and A2 is cyan) that allow the toxic A1 strand and its active site closer to r-RNA.

These amino acids are concerned in the active site of subunit A: Tyr-77 (black), Val-78 (red), Ser-112 (green), Val-162 (yellow), and Arg-170 (pink). The water molecule (blue) and formic acid (orange) are also connected to the active site.

Glycosidase cleavage is the process of breaking down the sugar on the r-RNA and releasing the adenine base. This occurs within the active site on A1. Also in the active site, there is one molecule of water and one of formic acid. Looking at the structure, it is likely that Arg-170 connects to the water molecule while Ser-112 and Val-78 connect to the formic acid. Also, Val-162 stabilizes this process, and Tyr-77 is the main catalyst involved. The end result of glycosidase cleavage is that the cell’s protein synthesis is inhibited or halted because the adenine base, when removed, changed the r-RNA sequence.

Subunit B comprises of chains B through F on the pdb file 1R4P. There are several binding sites that are the result of five identical chains creating a pentameter (similar to a star-like shape). It attaches to the globotriaosylceramide (GB3) on the cell membrane and signals for it to be brought into the cell. The cell membrane then engulfs the toxin in a bubble like structure acting as if it were a protein in the process of endocytosis.

This binding site consists of five potential parts. Of these, there are only four that contain a molecule of PPS (3-(1-pyridino)-1-propanesulfonate; shown in black), since one binding site conflicts with the amino acid Glu-184 in chain A therefore inhibiting the PPS bond. Also, two of the four binding sites also contains formic acid (shown in yellow) that help to mimic other effects in the binding site. Each of these effects is due to the pentamer that is formed from the five chains and their beta sheets, allowing the PPS molecules to "snap" right in place.

The amino acids for this binding site (in cyan) are: Asn-14, Asp-16, Thr-20, Glu-27, and Trp-29. There is one for each chain. The main contributor is the Trp in each chain that mainly holds the PPS in place, while the rest help this process along.

The main thing to note here is the first amino acid in each chain, Ala-1 (in pink), allows different reactions to ammonia groups that create a better affinity to reacting with carbohydrates. The disulfide bond also differs in that the 3rd and 56th residues (colored green) create a slightly different conformation, again allowing a more likelihood for carbohydrate bonding than other toxins, such as Stx1.

The two amino acids shown are: Trp-33 and Asn-34 (colored orange, one of each per the five chains). In this binding domain located at the pentamer's bottom, the tryptophan is the main component here. It helps regulate (along with another adjacent amino acid, asparagine) the Gb3 to bind here. One of these tryptophans even controls and "locks" in chain A in Subunit B as well. The alpha helices also displayed help create a core for chain A as well as lead to the bottom asparagine and tryptophan to help assist their binding along as well, though these tryptophans do tend to create different conformations and shapes, making the binding more adaptive in some mutations and strains.

References