Carbohydrate Binding Module Family 89 - Revision history

Mariana Morais at 10:21, 6 July 2023

2023-07-06T10:21:52Z

Mariana Morais at 10:18, 6 July 2023

2023-07-06T10:18:30Z

Mariana Morais at 10:16, 6 July 2023

2023-07-06T10:16:35Z

Elizabeth Ficko-Blean: /* Functionalities */

2023-06-29T13:50:58Z

Functionalities

Elizabeth Ficko-Blean: /* Functionalities */

2023-06-29T13:46:19Z

Functionalities

Elizabeth Ficko-Blean at 15:50, 28 June 2023

2023-06-28T15:50:44Z

Elizabeth Ficko-Blean: /* Family Firsts */

2023-06-28T15:49:28Z

Family Firsts

Elizabeth Ficko-Blean: /* Functionalities */

2023-06-28T15:47:28Z

Functionalities

Elizabeth Ficko-Blean: /* Structural Features */

2023-06-28T15:44:57Z

Structural Features

Elizabeth Ficko-Blean: /* Structural Features */

2023-06-28T15:43:38Z

Structural Features

@@ Line 21: / Line 21: @@
 == Structural Features ==
-[[File:Cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
+[[File:Cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure (PDB 7JVI [https://www.rcsb.org/structure/7JVI]). The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
 The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 7JVI]). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

@@ Line 21: / Line 21: @@
 == Structural Features ==
-[[File:cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
+[[File:Cbm89_cazypedia.png|thumb|300px|right|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
 The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 7JVI]). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

← Older revision		Revision as of 10:16, 6 July 2023
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	== Structural Features ==		== Structural Features ==

		+	[[File:cbm89_cazypedia.png\|thumb\|300px\|right\|'''Figure 1.''' CapCBM89 structure. The Ca<sup>2+</sup> (orange sphere), its coordinating residue (D344) and the two residues that impaired polysaccharide binding (Y62 and E82) are highlighted.]]
	The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 7JVI]). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .		The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>. A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns ([{{PDBlink}}7jvi PDB 7JVI]). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

@@ Line 25: / Line 25: @@
 == Functionalities ==
-In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a [[GH10]] domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-[[GH10]] and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The [[GH10]] domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the [[GH10]] domain to these substrates catalysis <cite>Cabral2022</cite>.
+In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a [[GH10]] domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-[[GH10]] and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The [[GH10]] domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the [[GH10]] domain to these substrates for catalysis <cite>Cabral2022</cite>.
 == Family Firsts ==

@@ Line 25: / Line 25: @@
 == Functionalities ==
-In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a [[GH10]] domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-[[GH10]] and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The [[GH10]] domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the [[GH10]] domain to these substrates catalysis <cite>Cabral2022</cite>. The most common associated glycoside hydrolases are from the [[GH10]] family.
+In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The most common associated glycoside hydrolases are from the [[GH10]] family. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a [[GH10]] domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-[[GH10]] and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The [[GH10]] domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the [[GH10]] domain to these substrates catalysis <cite>Cabral2022</cite>.
 == Family Firsts ==

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 ;First Identified: The first identified CBM89 member (CapCBM89) was from an uncultured Bacteroidaceae MAG57 recovered from the capybara gut microbiome <cite>Cabral2022</cite> .
-;First Structural Characterization: The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .
+;First Structural Characterization: The first CBM89 structure is [{{PDBlink}}7jvi PDB 7JVI], retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .
 == References ==