Difference between revisions of "Carbohydrate Binding Module Family 73"

Latest revision as of 13:14, 18 December 2021

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CAZy DB link
https://www.cazy.org/CBM73.html

Ligand specificities

Family 73 CBMs are modules of approximately 60 residues that are appended to bacterial enzymes associated to chitin degradation [1, 2, 3]. Binding to amorphous and crystalline α- and β-chitin has been demonstrated [1, 2]. The CBM73 module of the tri-modular LPMO, CjLPMO10A, binds tightly to α- chitin (Kd = 4.3 µM) and binding equilibrium was established within 15 minutes after mixing the protein and ligand [1].

Structural Features

Currently no NMR or crystal structure is available for CBM73s, but circular dichroism experiments of the CBM from the Vibrio cholera GlcNAc-binding protein (GbpA, VcLPMO10B) indicated a β-sheet containing structure [2]. Sequence alignment shows that the CBM73 are distantly related to chitin-binding modules belonging to the CBM5 family (type A). Despite low sequence similarity, conserved aromatic amino acids within the CBM5 family, responsible for substrate-binding [4], align well with similar residues in the CBM73 family (Figure 1A)[1, 3]. Two additional aromatic residues are found in the CBM73 family compared to the CBM5 family. Compatibly, a somewhat lower Kd for α-chitin was observed for the C-terminal CBM73 of the Cellvibrio japonicus LPMO (CjLPMO10A) relative to its internal CBM5 (Figure 1BC)[1].

Figure 1. (A) Multiple sequence alignment of CBM5s (grey) and CBM73s (yellow) from Cellvibrio japonicus (Cj), Cellvibrio mixus (Cm) and Streptomyces griseus (Sg). Conserved aromatic residues are labelled white on a blue background and the disulfide in CBM5s are shown above the alignment (S-S). (B) Modular organization of C. japonicus CBM73 containing enzymes. (C) Comparative binding of the CBMs from the C. japonicus LPMO (CjLPMO10A). Dissociation constants of 5.3 µM and 4.3 µM was obtained for α-chitin for the CBM5 and the CBM73, respectively [] , determined by solid state depletion assays. The figure was adapted from Forsberg et al. [].

Functionalities

Family 73 CBMs are found in Gram-negative bacteria from the phylum of Proteobacteria and are covalently attached to chitin degrading enzymes such as GH18 and GH19 chitinases [2, 5], AA10 chitin-oxidizing lytic polysaccharide monooxygenases [1, 2] and often in combination with a CBM5 chitin-binding module. In chitin degrading enzymes from C. japonicus, the family 73 CBMs are found internally as well as at the N- or C-terminus (Figure 1B). The CBM73 from CjLPMO10A, together with the CBM5, strongly promotes targeting and binding of crystalline α- and β-chitin as the LPMO domain alone binds weakly to its substrate. Removal of the two CBMs (CBM5 and CBM73) in CjLPMO10A reduces the lifetime of the catalytic AA10 domain and decreases the overall product yield. A CBM73 has also been found appended to a serine protease/peptidoglycan hydrolase from Vibrio vulnificus. Truncation of the two CBMs (CBM5 and CBM73) resulted in reduced peptidoglycan hydrolyzing activity but did not affect the protease activity [6].

Family Firsts

First Identified: Family CBM73 was first found as a C-terminal module of the tri-modular Cellvibrio japonicus chitin-oxidizing LPMO (AA10-CBM5-CBM73) [1].

First Structural Characterization: Hitherto, no structural information is available

References

All Medline abstracts: PubMed

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
-* [[Author]]: ^^^Zarah Forsberg^^^
+* [[Author]]: [[User:Zarah Forsberg|Zarah Forsberg]]
-* [[Responsible Curator]]:  ^^^Gustav Vaaje-Kolstad^^^
+* [[Responsible Curator]]:  [[User:Gustav Vaaje-Kolstad|Gustav Vaaje-Kolstad]]
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 == Ligand specificities ==
-Family 73 CBMs are modules of approximately 60 residues that are appended to bacterial enzymes associated to chitin degradation <cite>Forsberg2016 Wong2012 Tuveng2016</cite>. Binding to amorphous and crystalline α- and β-chitin has been demonstrated <cite>Forsberg2016 Wong2012</cite>.
+Family 73 CBMs are modules of approximately 60 residues that are appended to bacterial enzymes associated to chitin degradation <cite>Forsberg2016 Wong2012 Tuveng2016</cite>. Binding to amorphous and crystalline α- and β-chitin has been demonstrated <cite>Forsberg2016 Wong2012</cite>. The CBM73 module of the tri-modular LPMO, ''Cj''LPMO10A, binds tightly to α- chitin (Kd = 4.3 µM) and binding equilibrium was established within 15 minutes after mixing the protein and ligand  <cite>Forsberg2016</cite>.
 == Structural Features ==
-Currently no NMR or crystal structure is available for CBM73s, but circular dichroism experiments of the CBM from the ''Vibrio cholera'' GlcNAc-binding protein (GbpA, VcLPMO10B) indicated a  β-sheet containing structure <cite>Wong2012</cite>. Sequence alignment shows that the CBM73 are distantly related to chitin-binding modules belonging to the [[CBM5]] family  ([[Carbohydrate-binding_modules#Types|type A]]). Despite low sequence similarity, conserved aromatic amino acids within the [[CBM5]] family, responsible for substrate-binding <cite>Akagi2006</cite>, align well with similar residues in the CBM73 family (Figure 1)<cite>Forsberg2016 Tuveng2016</cite>. Two additional aromatic residues are found in the CBM73 family compared to the CBM5 family. Compatibly, a somewhat lower ''K''d for α-chitin was observed for the C-terminal CBM73 of the ''Cellvibrio japonicus'' LPMO (''Cj''LPMO10A) relative to its internal CBM5 <cite>Forsberg2016</cite>.
+Currently no NMR or crystal structure is available for CBM73s, but circular dichroism experiments of the CBM from the ''Vibrio cholera'' GlcNAc-binding protein (GbpA, VcLPMO10B) indicated a  β-sheet containing structure <cite>Wong2012</cite>. Sequence alignment shows that the CBM73 are distantly related to chitin-binding modules belonging to the [[CBM5]] family  ([[Carbohydrate-binding_modules#Types|type A]]). Despite low sequence similarity, conserved aromatic amino acids within the [[CBM5]] family, responsible for substrate-binding <cite>Akagi2006</cite>, align well with similar residues in the CBM73 family (Figure 1A)<cite>Forsberg2016 Tuveng2016</cite>. Two additional aromatic residues are found in the CBM73 family compared to the CBM5 family. Compatibly, a somewhat lower ''K''d for α-chitin was observed for the C-terminal CBM73 of the ''Cellvibrio japonicus'' LPMO (''Cj''LPMO10A) relative to its internal CBM5 (Figure 1BC)<cite>Forsberg2016</cite>.
-[[Image:CBM73 fig1.png|thumb|right|600px|'''Figure 1.''' (A) Multiple sequence alignment of CBM5s (grey) and CBM73s (yellow) from ''Cellvibrio japonicus'' (Cj), ''Cellvibrio mixus'' (Cm) and ''Streptomyces griseus'' (Sg). Conserved aromatic residues are labelled white on a blue background and the disulfide in CBM5s are shown above the alignment (S-S). (B) Modular organization of ''C. japonicus'' CBM73 containing enzymes. (C) Comparative binding of the CBMs from the ''C. japonicus'' LPMO (CjLPMO10A). Dissociation constants of 5.3 µM and 4.3 µM was obtained for α-chitin for the CBM5 and the CBM73, respectively <cite>Forsberg2016</cite>. The figure was adapted from Forsberg et al. <cite>Forsberg2016</cite>.          ]]
+[[Image:CBM73 fig1.png|thumb|right|600px|'''Figure 1.''' (A) Multiple sequence alignment of CBM5s (grey) and CBM73s (yellow) from ''Cellvibrio japonicus'' (Cj), ''Cellvibrio mixus'' (Cm) and ''Streptomyces griseus'' (Sg). Conserved aromatic residues are labelled white on a blue background and the disulfide in CBM5s are shown above the alignment (S-S). (B) Modular organization of ''C. japonicus'' CBM73 containing enzymes. (C) Comparative binding of the CBMs from the ''C. japonicus'' LPMO (CjLPMO10A). Dissociation constants of 5.3 µM and 4.3 µM was obtained for α-chitin for the CBM5 and the CBM73, respectively <cite>Forsberg2016</cite> , determined by solid state depletion assays. The figure was adapted from Forsberg et al. <cite>Forsberg2016</cite>.          ]]
 == Functionalities ==
-CBM73s are found in Gram-negative bacteria from the phylum of Proteobacteria and are covalently attached to chitin degrading enzymes such as GH18 and GH19 chitinases <cite>Wong2012 Deboy2008</cite>, AA10 chitin-oxidizing lytic polysaccharide monooxygenases <cite>Forsberg2016 Wong2012</cite> and often in combination with a CBM5 chitin-binding module. In chitin degrading enzymes from ''C. japonicus'', the CBM73s are found internally as well as in the N- or C-terminus (Fig. 1). The CBM73 from ''Cj''LPMO10A (together with the CBM5) strongly promotes targeting and binding of crystalline α- and β-chitin as the LPMO domain alone binds weakly to its substrate. Removal of the two CBMs (CBM5 and CBM73) in ''Cj''LPMO10A reduces the lifetime of the catalytic AA10 domain and decreases the overall product yield. A CBM73 has also been found appended to a serine protease/peptidoglycan hydrolase from ''Vibrio vulnificus''. Truncation of the two CBMs (CBM5 and CBM73) resulted in reduced peptidoglycan hydrolyzing activity but did not affect the protease activity <cite>Lim2011</cite>.
+Family 73 CBMs are found in Gram-negative bacteria from the phylum of Proteobacteria and are covalently attached to chitin degrading enzymes such as [[GH18]] and [[GH19]] chitinases <cite>Wong2012 Deboy2008</cite>, [[AA10]] chitin-oxidizing lytic polysaccharide monooxygenases <cite>Forsberg2016 Wong2012</cite> and often in combination with a [[CBM5]] chitin-binding module. In chitin degrading enzymes from ''C. japonicus'', the family 73 CBMs are found internally as well as at the N- or C-terminus (Figure 1B). The CBM73 from ''Cj''LPMO10A, together with the [[CBM5]], strongly promotes targeting and binding of crystalline α- and β-chitin as the LPMO domain alone binds weakly to its substrate. Removal of the two CBMs ([[CBM5]] and CBM73) in ''Cj''LPMO10A reduces the lifetime of the catalytic [[AA10]] domain and decreases the overall product yield. A CBM73 has also been found appended to a serine protease/peptidoglycan hydrolase from ''Vibrio vulnificus''. Truncation of the two CBMs ([[CBM5]] and CBM73) resulted in reduced peptidoglycan hydrolyzing activity but did not affect the protease activity <cite>Lim2011</cite>.
 == Family Firsts ==
 ;First Identified
-:Family CBM73 was first found as a C-terminal module of the tri-modular ''Cellvibrio japonicus'' chitin-oxidizing LPMO (AA10-CBM5-CBM73) <cite>Forsberg2016</cite>.
+:Family CBM73 was first found as a C-terminal module of the tri-modular ''Cellvibrio japonicus'' chitin-oxidizing LPMO ([[AA10]]-[[CBM5]]-CBM73) <cite>Forsberg2016</cite>.
 ;First Structural Characterization