| Challenge | Sheridanse,
Team Brain Blast | 2017-04-14 15:03:07 CDT | Fig 4: Did not describe overlap in the catalytic domain of CD27L & PlyPSA; did not describe similarities in secondary structures. Also did not talk about extensions and loops that show an increase in substrate binding area. Should elaborate on how PlyPSA has the molecular surface representation in the same orientation as CD27L.
| None, yet. |
| Challenge | Yonasm,
Team The Lysogenizers | 2017-04-12 10:25:07 CDT | How does the catalytic domain determing the catalytic activity of the protein CD27L versus that of the bacterial strains.
What were the results of the alignment in figure 5, between protein CD27L with Clostridia.
| None, yet. |
Public
Assessment | AAJohnson | 2017-05-06 05:49:25 CDT | IMP (by domain truncation) doesn't lead to the data showing the GO term you selected. This annotation should use an evidence code for the piece of data that specifically shows you this protein is an N-acetyl-L-alanine amidase.
Your should strengthen the details of your notes to clearly state how you know from the evidence that this protein is an N-acetyl-L-alanine amidase- identify whether conserved residues that contribute to function have been identified.
Figure 2 doesn't support that specific GO term and you could separate that into a different annotation for this protein with a less specific GO term.
| Requires Changes
✗ Go term
✗ Evidence
✗ Notes
|
Public
Assessment | DanielRenfro | 2017-04-17 10:53:18 CDT | This annotation has been flagged because it has been edited since last assessment
| Qualifier |
GO ID |
GO term name |
Reference |
Evidence Code |
with/from |
Aspect |
Notes |
Status
|
|
GO:0008745 |
N-acetylmuramoyl-L-alanine amidase activity |
PMID:21803993 |
IMP: Inferred from Mutant Phenotype |
|
F |
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. |
complete
CACAO 12506
| on 9CAUD:B6SBV8
| Flagged
|
Public
Assessment | DanielRenfro | 2017-04-17 10:51:54 CDT | This annotation has been flagged because it has been edited since last assessment
| Qualifier |
GO ID |
GO term name |
Reference |
Evidence Code |
with/from |
Aspect |
Notes |
Status
|
|
GO:0008745 |
N-acetylmuramoyl-L-alanine amidase activity |
PMID:21803993 |
IMP: Inferred from Mutant Phenotype |
|
F |
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 as 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. |
complete
CACAO 12506
| on 9CAUD:B6SBV8
| Flagged
|
