User:Ramanand

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
requireschanges	9CAUD:B6SBV8	2017-04-09 08:14:04 CDT	GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)	PMID:21803993	ECO:0000315 mutant phenotype evidence used in manual assertion	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
requireschanges	BARHE:A0A0H3M3F4	2017-04-30 22:23:08 CDT	GO:0008745 N-acetylmuramoyl-L-alanine amidase activity (F)	PMID:22715947	ECO:0000315 mutant phenotype evidence used in manual assertion	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.	challenge
requireschanges	NOSP7:B2J2S4	2017-04-30 22:06:06 CDT		PMID:26833702	ECO:0000315 mutant phenotype evidence used in manual assertion	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

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Annotations challenged by Ramanand

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