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Category:Team Viridae

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
requireschanges9CAUD:B6SBV8Ramanand, Team Viridae2017-04-09 08:14:04 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)PMID:21803993IMP

Figures 2a and 2b shows the strain-specific, GFP-labeled, full-length protein as well as the N-terminus truncation of the full-length protein binding to the cell wall of C.difficile. Figure 2c shows the lytic activity of these two forms of CD27L against C. difficile cells compared to autolytic activity present in the buffer control. Figure 3 shows two residues, L130 and Y131, in the crystal structure of the catalytic domain of CD27L that are conserved for amidases specific to Clostridia. Figure 4 shows that there is a similar backbone structure between the N-terminus CD27L and another amidase, PlyPSA, specific to Listeria monocytogenes. A DALI analysis conducted by the authors reveals that the two structures are identical for 171 residues with a Z score of 24.2 indicating a strong structural match with an amidase protein. There is a 30% sequence identity and identical topologies between the catalytic domains of these two amidases. The structures differ in that the N-terminus of CD27L has larger loop extensions, and thereby larger substrate binding domain area, than PlyPSA. Figures 4b and 4c shows that the CD27L N-terminus surface is more positively charged than the surface of PlyPSA. However, these differences point to differences in substrate binding accessibility rather than differences in actual catalytic function. Figure 5 shows sequence homology between CD27L and 14 unique C. difficile-targeting endolysin proteins through a BLAST search. In addition figure 5 also shows that amongst these endolysin proteins the L130 and Y131 in the substrate binding domain of CD27L are conserved amongst the 14 unique proteins.

challenge
requireschangesSTRGL:LYSM1Ikrama2, Team Viridae2017-04-23 19:22:49 CDT0008152 metabolic process (P)PMID:11427528IDA

The metabolic process has to do with the structure of the overall protein. The structure of Cellosyl comprised to a single domain,is demonstrated in figure 2. Where it is shown that the structure is comprised of eight beta strands and six alpha helices. Shown with the strands forming the staves of the barrel and the helices located around it. Helices are depicted in red, loops in green, the parallel βeta-strands in blue, and the antiparallel βeta-strand is highlighted in yellow.

challenge
requireschanges9CAUD:D9ZNF3Ikrama2, Team Viridae2017-04-23 22:24:19 CDTGO:0009253 peptidoglycan catabolic process (P)PMID:26683375IMP

In figure 4 they show a sequence alignment on the nucleotide level of CTP1L and CS74L. In the figure there are other related endolysins shown that are present. The putative Shine-Dalgarno region is shown in figure 4a and 4b in the red. It also indicates that the start codon is GTG. The nucleotide sequence used during E. coli expression of when they did the sequence alignment was derived from the original bacteriophage DNA. To test whether the wild-type sequence encoded a secondary translation site to the wild type.

challenge
flagged9CAUD:B6SBV8Syedsa, Team Viridae2017-04-29 17:09:16 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)PMID:21803993IMP

Figures 1a, 1b, and 1c show how the lytic activity and specificity were effected by truncation. Figure 1a goes in depth on how the N- and C-terminal truncations of endolysin CD27L were produced as His-tagged proteins. Figure 1b displays the CD27L (1–179) and the full CD27L both failed to lyse C. tyrobutyricum. Figure 1c gives the assays of 10 the μg Ni-NTA-purified buffer incubated cells.

challenge
flaggedBPPHX:A3FJT0Syedsa, Team Viridae2017-04-29 23:35:38 CDTGO:0004857 enzyme inhibitor activity (F)PMID:28446197IDA

Table 3 shows the activity levels of B. licheniformis. The activity percentages show how growth is inhibited by 0.5 µM of the E protein when compared to the normal growth of B. licheniformis after 6 hours. The table shows PduP-E from Ec3087 having the greatest inhibition after induction of 0.1 mM Rha.

challenge
requireschangesSTRGL:LYSM1Chaudrye, Team Viridae2017-04-30 18:48:31 CDTGO:0003796 lysozyme activity (F)PMID:11427528IDA

Figure 1 displays that unlike other lysozymes (HEWL, GEWL, and T4L-types), the Ch-type lysozymes have both Beta-1,4-N-acetyl- and Beta-1,4,-N,6-O-diacetylmuramidase activities. Due to this characteristic they are able to cleave the 6-O-acetylated peptidoglycans. This icnludes the peptiodglycans that are present in cell walls of Staphylococcus aureus.

Figure 2 displays that the structure of Cellosyl contributes to its function. Figure two shows that Cellosyl comprises a single domain. The enzyme is shown to have a beta/alpha-barrel fold. This is different than many other enzymes which have (Beta/alpha)8-barrels. All of these specific folds allow for the active site to be locate at the C-terminal end of the beta-barrel. Figure 3 compares the amino acid sequence of various Ch-type lysozymes and it supports that the active site is located at the C-terminal end of the Beta-barrel. It does so because it shows that the amino acids at the C-terminal ends of Beta1 and Beta4 are highly conserved among lysozymes from bacteria and Chalaropsis. Figure 4 displays how the charges are distributed on the surface of Cellosyl and how that impacts it's lysozyme activity. Due to the grove in the substrate-binding site, there is a high negative electrostatic potential. This is developed to the deep hole.

challenge
unacceptableBACAN:Q81YZ2Chaudrye, Team Viridae2017-04-30 19:12:06 CDTGO:0003796 lysozyme activity (F)PMID:21816821IDA

Figure 1 displays that the two glycan chains are cross-peptide linked. The bond formed is what the amidase lysins target . It displays the cleavage positions of other common lysins in comparison to this lysin. Through this figure one can see that the gram-positive bacteria displays species as well as strain specific "secondary cell wall polymers" (SCWPS). These insert themselves into the lipid bilayer, which changes the appearance and the charge of the outer envelope.

Figure 2 was used in order to compare this lysin to two homologous amidase lysins to see the similar structures and distinct behaviours between them (PlyL and XlyA). Due to the high structural similarity, a test was conducted to see whether the innate catalytic acitivty of XlyA was similar to that of PlyL. Figure 3 displays that XlyA:plyL chimera failed to lyse B. subtilis, however it did lyse B. cereus.

challenge
requireschangesNOSP7:B2J2S4Ramanand, Team Viridae2017-04-30 22:06:06 CDTPMID:26833702IMP

Figure 1C shows AmiC2 labeled with FITC mostly localizes to newly formed septal junctions verse older junctions showing AmiC2 amidase related activity in Nostoc Punctiforme. Likewise figure 1D shows localization of AmiC2 to septal junctions of different developmental stages. Figure 2B shows lytic activity of the catalytic domain of AmiC2. Figure 3 shows an alpha beta fold motif present in other amidase_3 enzymes. Figure 4A and 4B shows the residues that are conserved in this protein with other amidase family proteins.

challenge
requireschangesBARHE:A0A0H3M3F4Ramanand, Team Viridae2017-04-30 22:23:08 CDTGO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)PMID:22715947IMP

Figure 1D shows that AmiB mutants have lytic activity. This indicates that these mutants which are increasingly in its active state have increased amidase activity. This increase in unregulated amidase activity results in cell lysis. Figure 2 shows sequence alignment identity and similarities with phage endolysins, lysis enzymes for sporulating bacteria, and lytic enzymes for gram-negative proteobacteria. When compared to phage endolysin there are similar (grey) and identical residues (black) as well as a 50 amino acid section that is not present in phage endolysins that is considered to be used for regulation. The function of this regulation section is described in Figure 3C an alpha helical domain that blocks the substrate from the zinc ion in the active site. Figure 3A and B shows that the core structure of this enzyme is similar to other amidases with exception to the 50 amino acid stretch. Figure S3A (supplemental 3A) shows that three residues that coordinates to the zinc ion in the active site is conserved for LytC-type amidases. Figure 4a shows increased peptidoglycan hydrolase activity for PG sacculi compared to wildtype AmiB when incubated with AmiB mutants that have destabilized regulatory mechanism.

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Pages in category "Team Viridae"

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