Category:Team ZIRTS

Figure 2B shows the structural homolog of XlyA. XlyA is an endolysin. Figure 2B shows structural similarity between XlyA and another amidase lysin, PlyL.

Figure 3B shows the sequence of the XlyA catalytic domain is similar to the catalytic domain of PlyL, another endolysin. The red boxes show XlyA contains catalytic and substrate recognition residues similar or identical to PlyL.The asterisks indicate base pair identity between XlyA and PlyL sequences. The colons indicate base pair similarity between XylA and PlyL. The high similarity and identity within the sequence alignment and secondary structure assignments of XylA and PlyL support the lysozyme function of XylA.

The HHpred E-value is 3.5E^-25. The daughter cells in the paper require peptidoglycan catabolic process to separate. A fractured cell wall released lysosome and mutanolysin digestion. This related in the long amino acid chains breaking apart.

In Figure 1, SCWPs are typically attached via the C-6 hydroxyl group on MurNac. The presence of the hydroxyl group is indication of hydrolase activity. The d-Glu uses its γ-carboxyl to makes an amide bond with m-DAP. The presence of a carboxyl group, which contains bonds used in hydrolase activity. The γ-carboxyl is used similarly to an enzyme in the process of making an amide bond.

Figure 6a shows a scatter plot diagram of electron-density map vs. the B factor in P22 lysozyme. The peak densities for N and O atoms decreases with the atomic temperature factor; the distribution of C atoms moves away from decay. Figure 6b shows C, N, and O decreasing very similarly exponentially.

Figure 4C shows the four mutation sites in PlyBa04. In addition, a glycan muropeptide fragment is shown, connecting it to pneumococcal phage lysin. The PlyBa04 (blue) and PlyB (gray) catalytic domains are identified, showing their similarity using heavy atom methods. They are glycosyl hydrolases, having a mostly parallel central eight-stranded beta-barrel with a helix/extended loop connected the rest of the seven parallel strands. The seventh and eighth strands are connected by a short beta-hairpin, creating the anti parallel strand.

the Effect of S-layer—Was compared the effects of PlyL and they were closely related PlyG with 96% identical in the catalytic domain , and 63% in the CBD.

Figure 5A: shows how the cell killing activity of the full length which is the top bar and the catalytic domain the second bar of plyL and plyG against B. anthracis Sterne, B. anthracis (sap) mutant deficient in S-layer synthesis,and B. subtilis. Each B strains consist of 0.4uM of lysin concentration. From the graph we can also conclude that PlyG(CAT) killed Sterne more than twice as fast as PlyG(FULL). The full length graph show that with out S-layer, PlyL and plyG can still be active. The blue bar is plyL (full) and red bar is plyL(CAT). the light blue bar is plyG (full) and green bar is plyG(CAT). PlyL(CAT) had a higher lytic activity than PlyL(FULL), and PlyG(CAT) killed Sterne more than twice as fast as PlyG (FULL)

Figure 1 shows the use of carboxyl groups on MurNac moiety to for an amide bond with α-amino group of l-Ala. The chemical reaction's use of the carboxyl groups to form additional bonds between peptides.

In Figure 2A, both XylA and PlyL’s structures were being compared which indicated that the two of these proteins are amidase lysins. In this particular figure(2A), their functions were being tested based on their ability to lyse B. Subtilis. They found that the catalytic domain of PlyL which was indicated in the paper by “PlyL CAT” had homologous lysing abilities to the entirety of XylA.

The effect of B-anthracis s-layer on lytic activity and whole cell binding by using two homologous amidases plyL and plyG are show in these figures. Figure 5A: shows the pulling down of whole cell wall binding assay using a tagged CBD of plyL and plyG infecting wild B. anthracis, B. cereus 4342 B. and subtilis. Also using it as a control as a architecture. Lower gels are Western blots using anti-His antibody, and the Upper gels show expression of Sap protein, with markers at 59 and 107 kDa.

The HHpred predicted E-value for this is 1.2E-32. In the literature Fig. 1 compares Candida albicans' Dihydrofolate Reductase to Pneumocystis carinii and they share a 34% match with each other's amino acid sequence. The activity also matches the yeast gene DFR1.

Figure 3A shows the bactericidal activity of lysin XlyA against B. cereus and B. subtillis. Figure 3C illustrates the residues of the XlyA catalytic domain. It is shown in this figure some structures present in the XylA catalytic domain are identical to those of PlyL, another endolysin.