Update avs.md

content/3.defense-systems/avs.md

@@ -22,10 +22,13 @@ relevantAbstracts:
 # Avs
 
 ## Description 
-Avs proteins are members of the STAND (signal transduction ATPase with numerous domains) superfamily of P-loop NTPases, which play essential roles in innate immunity and programmed cell death in eukaryotes (:ref{doi=10.1038/sj.cdd.4400991, 10.1016/j.jmb.2004.08.023}). STAND ATPases include nucleotide-binding oligomerization domain-like receptors (NLRs) in animal inflammasomes and plant resistosomes. Bacterial Avs share a common tripartite domain architecture with eukaryotic NLR, typically consisting of a central ATPase, a C-terminal sensor with superstructure-forming repeats, and an N-terminal effector involved in inflammation or cell death. They are very similar to other bacterial defense systems: bNACHT (https://defense-finder.pasteur.cloud/wiki/defense-systems/nlr), CARD_NLR (https://defense-finder.pasteur.cloud/wiki/defense-systems/card_nlr) , Rst_TIR-NLR (https://defense-finder.pasteur.cloud/wiki/defense-systems/rst_tir-nlr). 
+Avs proteins are members of the STAND (signal transduction ATPase with numerous domains) superfamily of P-loop NTPases, which play essential roles in innate immunity and programmed cell death in eukaryotes :ref{doi=10.1038/sj.cdd.4400991, 10.1016/j.jmb.2004.08.023}. STAND ATPases include nucleotide-binding oligomerization domain-like receptors (NLRs) in animal inflammasomes and plant resistosomes. Bacterial Avs share a common tripartite domain architecture with eukaryotic NLR, typically consisting of a central ATPase, a C-terminal sensor with superstructure-forming repeats, and an N-terminal effector involved in inflammation or cell death. They are very similar to other bacterial defense systems: [bNACHT](/defense-systems/nlr), [CARD_NLR](/defense-systems/card_nlr) , [Rst_TIR-NLR](/defense-systems/rst_tir-nlr). 
 
 ## Molecular mechanism
-To note: two classifications of Avs systems were proposed. The first one (:ref{doi=10.1126/science.aba0372}) distinguishes 5 types of Avs based on their effector domain. This is the classification used in Defense Finder right now, and in the following wiki entry unless stated otherwise. Considering the modular aspect of the effector domain, a new classification based on the homology of the NTPase and C terminal sensor domain, and not on the effector domain, has been proposed more recently (:ref{doi=10.1126/science.abm4096}) and is the one used in this description of the mechanism. This second classification defines 4 different types, that do not represent the whole diversity of Avs proteins but only the 4 characterized types.
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+Two classifications of Avs systems were proposed. The first one :ref{doi=10.1126/science.aba0372} distinguishes 5 types of Avs based on their effector domain. This is the classification used in Defense Finder right now, and in the following wiki entry unless stated otherwise. Considering the modular aspect of the effector domain, a new classification based on the homology of the NTPase and C terminal sensor domain, and not on the effector domain, has been proposed more recently :ref{doi=10.1126/science.abm4096} and is the one used in this description of the mechanism. This second classification defines 4 different types, that do not represent the whole diversity of Avs proteins but only the 4 characterized types.
+::
 
 Similar to their eukaryotic counterparts, Avs proteins utilize their C-terminal sensor domains to bind to pathogen-associated molecular patterns (PAMPs). Specifically, Avs1, Avs2, and Avs3 bind to monomers of the large terminase subunit of tailed phages, which account for approximately 96% of all phages, whereas Avs4 binds to monomers of the portal protein. The helical sensor domains of Avs1-4 can recognize diverse variants of terminase or portal proteins, with less than 5% sequence identity in some cases. Binding is mediated by shape complementarity across an extended interface, indicating fold recognition. Additionally, Avs3 directly recognizes active site residues and the ATP ligand of the large terminase.