Category:Team Brain Blast

The N-terminal enzymatically active domain (EAD) of an endolysin is the source of it's catalytic behavior, and in this sense, will determine evidence of hydrolytic activity. Endolysin PLY500 has displayed L-alanoyl-D-glutamate endopeptidase activity in Listeria phages. Listeria phage PLY118 (Listeria phage A118) shows 30% amino acid alignment with PLY500 in terms of EAD (fig.1, indicated by overhead black bars). While there is no relations between the C-terminal domains (structural evidence) of PLY500 and PLY118, the genes active in binding the catalytic Zn2+ ion and LAS protein identification are conserved within this 30% PLY118 matching amino acid sequence. From this information it is likely that the N-terminal domains of PLY118 and PLY500 are similar enough to be classified in the same functional LAS family.

Figure 1 of the paper compares proteins PLY500 and PLY118. According to the introduction of the paper PLY500 is an endolysin that consists of a C-terminal cell wall binding domain and a N-terminal enzymatically active domain (EAD). The cell wall binding domain is for recognizing and binding to specific bacterial cell surfaces. PLY118 is another protein from a related Listeria phage, A118. PLY118 is a peptidase in A118. Both of these proteins have unrelated cell wall binding domains but their endopeptidase has a clear sequence homology to EAD500. EAD500 was recently shown to be chromosomally encoded in Bacillus subtilis.

It is inferred that the protein VanX has dipeptidase properties based on it's similarities in structure to the known murine Sonic Hedgehog (an N-terminal fragment composing the hydrolytic functionality) and the D-ala-D-ala-carboxypeptidase S.Albus(composing the peptidase functionality). Fig 6A shows the alignment comparison of all three; VanX and MSH overlap for 92 alpha carbons, and VanX and S.Albus overlap for 114 alpha carbons. 6B shows at least 7 major homologous overlaps between VanX, MSH and S.Albus. In 6A, the superfamily relationship amongst VanX, MSH and S.Albus is validated by the similarities in active site location;in VanX it is located within residues 83-111, which aligns almost exact with MSH and S.Albus.

Indian Hedgehog proteins facilitate binding to the patched (PTC1)receptor in order to interact with foreign cells. Mutations of Indian Hedgehog (IHH) proteins are the cause of the disorder Brachydactyly type A1(BDA1), which physically causes an underdevelopment in digits where the second and third phalanges are either fused together or do not completely form. Fig.4 shows the effects on receptor-binding ability to a patched receptor when the hedgehog protein hosts a mutation. Fig.4A graphs the percentage of protein binding to a PTC1 receptor versus the amount of the protein present (in respect to the wild type human protein, and two BDA1 mutation proteins). Fig. 4B shows that the BDA1 mutations have a significantly decreased binding activity level in comparison to the human protein. These results are analyzed from figure S2, which displays the incubated assay results of the wild type and mutated proteins.

This protein is carboxypeptidase activity because in the introduction of the paper, the terminal D-alanine of the nascent pentapeptide stem is hydrolyzed by DD-carboxypeptidases from the class C penicillin binding protein. Also membrane preparations of Bacillus subtilis have shown strong LD-carboxypeptidase against cell wall derived tetrapeptides.