Carbohydrate Binding Module Family 50 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:19:08Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Takayuki Ohnuma at 00:02, 24 June 2014

2014-06-24T00:02:57Z

Takayuki Ohnuma at 04:32, 20 June 2014

2014-06-20T04:32:34Z

Harry Brumer: added PDB links

2014-06-19T15:34:40Z

added PDB links

Harry Brumer at 15:30, 19 June 2014

2014-06-19T15:30:40Z

Alicia Lammerts van Bueren at 18:44, 17 June 2014

2014-06-17T18:44:00Z

Alicia Lammerts van Bueren at 18:40, 17 June 2014

2014-06-17T18:40:59Z

Alicia Lammerts van Bueren: edits of cbm50 page

2014-06-17T18:37:33Z

edits of cbm50 page

Takayuki Ohnuma at 01:24, 30 May 2014

2014-05-30T01:24:44Z

Takayuki Ohnuma at 12:05, 29 May 2014

2014-05-29T12:05:56Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]:   ^^^Takayuki Ohnuma^^^ and ^^^Toki Taira^^^
+* [[Author]]:   [[User:Takayuki Ohnuma|Takayuki Ohnuma]] and [[User:Toki Taira|Toki Taira]]
-* [[Responsible Curator]]:  ^^^Takayuki Ohnuma^^^
+* [[Responsible Curator]]:  [[User:Takayuki Ohnuma|Takayuki Ohnuma]]
 ----

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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]]:   ^^^Takayuki Ohnuma^^^ and ^^^Toki Taira^^^
 * [[Responsible Curator]]:  ^^^Takayuki Ohnuma^^^

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 == Structural Features ==
-CBM50 modules are about 50 amino acids long. The three-dimensional structures of three CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (PDB entries: [{{PDBlink}}1e0g 1e0g]  <cite>Bateman2000</cite>, [{{PDBlink}}2mkx 2mkx] and [{{PDBlink}}4pxv 4pxv]). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma ''et al''. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments <cite>Ohnuma2008</cite>. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
+CBM50 modules are about 50 amino acids long. The three-dimensional structures of several CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (example PDB entries: [{{PDBlink}}1e0g 1e0g]  <cite>Bateman2000</cite>, [{{PDBlink}}2mkx 2mkx] and [{{PDBlink}}4pxv 4pxv]). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma ''et al''. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments <cite>Ohnuma2008</cite>. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
 == Functionalities ==

@@ Line 20: / Line 20: @@
 == Structural Features ==
-CBM50 modules are about 50 amino acids long. The three-dimensional structures of three CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (PDB entries: 1E0G  <cite>Bateman2000</cite>, 2MKX and 4PXV). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma ''et al''. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments <cite>Ohnuma2008</cite>. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
+CBM50 modules are about 50 amino acids long. The three-dimensional structures of three CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (PDB entries: [{{PDBlink}}1e0g 1e0g]  <cite>Bateman2000</cite>, [{{PDBlink}}2mkx 2mkx] and [{{PDBlink}}4pxv 4pxv]). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma ''et al''. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments <cite>Ohnuma2008</cite>. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
 == Functionalities ==
@@ Line 29: / Line 29: @@
 CBM50s are also known as LysM domains. The LysM domain was first identified in lysozyme from ''Bacillus phage'' f29 <cite>Garvey1986</cite>. LysM domains were first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an ''N''-terminal LysM domain from ''Pteris ryukyuensis'' chitinase-A <cite>Ohnuma2008</cite>.
 ;First Structural Characterization
-The first three-dimensional structure of CBM50 module was determined for the LysM domain from ''E. coli'' membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: 1E0G) by NMR spectroscopy <cite>Bateman2000</cite>.
+The first three-dimensional structure of CBM50 module was determined for the LysM domain from ''E. coli'' membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: [{{PDBlink}}1e0g 1e0g]) by NMR spectroscopy <cite>Bateman2000</cite>.
 == References ==

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 == Ligand specificities ==
-CBM50 modules are also known as LysM domains. They bind to the N-acetylglucosamine residues in bacterial peptidoglycans and in chitin. For example CBM50 of ''Lactococcus lactis'' ''N''-acetylglucosaminidase AcmA was shown to bind to the glycan chain of bacterial peptidoglycans, a β-1,4 linked heteropolymer of alternating ''N''-acetylglucosamine (GlcNAc) and ''N''-acetylmuramic acid (MurNAc) <cite>Steen2003</cite>. A CBM50 module from ''Pteris ryukyuensis'' chitinase-A (PrChi-A) was demonstrated to bind to chitin, a β-1,4-linked homopolymer of GlcNAc <cite>Onaga2008</cite>. From isothermal titration calorimetry, the CBM50 module from PrChi-A was found to bind to (GlcNAc)<sub>n</sub> (n=4,5) with the binding stoichiometry of 1:1, whereas no significant binding heat was observed for the binding to (GlcNAc)<sub>2</sub> <cite>Ohnuma2008</cite>. The binding site of the CBM50 module can accommodate at least three saccharide units.
+CBM50 members are also known as LysM domains. They bind to the N-acetylglucosamine residues in bacterial peptidoglycans and in chitin. For example CBM50 of ''Lactococcus lactis'' ''N''-acetylglucosaminidase AcmA was shown to bind to the glycan chain of bacterial peptidoglycans, a β-1,4 linked heteropolymer of alternating ''N''-acetylglucosamine (GlcNAc) and ''N''-acetylmuramic acid (MurNAc) <cite>Steen2003</cite>. A CBM50 module from ''Pteris ryukyuensis'' chitinase-A (PrChi-A) was demonstrated to bind to chitin, a β-1,4-linked homopolymer of GlcNAc <cite>Onaga2008</cite>. From isothermal titration calorimetry, the CBM50 module from PrChi-A was found to bind to (GlcNAc)<sub>n</sub> (n=4,5) with the binding stoichiometry of 1:1, whereas no significant binding heat was observed for the binding to (GlcNAc)<sub>2</sub> <cite>Ohnuma2008</cite>. The binding site of the CBM50 module can accommodate at least three saccharide units.
 == Structural Features ==

@@ Line 27: / Line 27: @@
 == Family Firsts ==
 ;First Identified
-CBM50 is also known as LysM domains. The LysM domain was first identified in lysozyme from ''Bacillus phage'' f29 <cite>Garvey1986</cite>. LysM domains were first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an ''N''-terminal LysM domain from ''Pteris ryukyuensis'' chitinase-A <cite>Ohnuma2008</cite>.
+CBM50s are also known as LysM domains. The LysM domain was first identified in lysozyme from ''Bacillus phage'' f29 <cite>Garvey1986</cite>. LysM domains were first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an ''N''-terminal LysM domain from ''Pteris ryukyuensis'' chitinase-A <cite>Ohnuma2008</cite>.
 ;First Structural Characterization
 The first three-dimensional structure of CBM50 module was determined for the LysM domain from ''E. coli'' membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: 1E0G) by NMR spectroscopy <cite>Bateman2000</cite>.

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-A CBM50 module, also known as LysM domain, from Lactococcus lactis N-acetylglucosaminidase AcmA was shown to bind to the glycan chain of bacterial peptidoglycans, a -1,4 linked heteropolymer of alternating N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) [1]. A CBM50 module from Pteris ryukyuensis chitinase-A (PrChi-A) was demonstrated to bind to chitin, a -1,4-linked homopolymer of GlcNAc [2]. CBM50 modules appear to recognize the GlcNAc residue of these polysaccharides. From isothermal titration calorimetry, the CBM50 module from PrChi-A was found to bind to (GlcNAc)n (n=4,5) with the binding stoichiometry of 1:1, whereas no significant binding heat was observed for the binding to (GlcNAc)2 [3]. The binding site of the CBM50 module can accommodate at least three saccharide units.
+A CBM50 module, also known as LysM domain, from ''Lactococcus lactis'' ''N''-acetylglucosaminidase AcmA was shown to bind to the glycan chain of bacterial peptidoglycans, a β-1,4 linked heteropolymer of alternating ''N''-acetylglucosamine (GlcNAc) and ''N''-acetylmuramic acid (MurNAc) <cite>Steen2003</cite>. A CBM50 module from ''Pteris ryukyuensis'' chitinase-A (PrChi-A) was demonstrated to bind to chitin, a β-1,4-linked homopolymer of GlcNAc <cite>Onaga2008</cite>. CBM50 modules appear to recognize the GlcNAc residue of these polysaccharides. From isothermal titration calorimetry, the CBM50 module from PrChi-A was found to bind to (GlcNAc)<sub>n</sub> (n=4,5) with the binding stoichiometry of 1:1, whereas no significant binding heat was observed for the binding to (GlcNAc)<sub>2</sub> <cite>Ohnuma2008</cite>. The binding site of the CBM50 module can accommodate at least three saccharide units.
 == Structural Features ==
-CBM50 modules are about 50 amino acids long. The three-dimensional structures of three CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (PDB entries: 1E0G [4], 2MKX and 4PXV). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma et al. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments [3]. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
+CBM50 modules are about 50 amino acids long. The three-dimensional structures of three CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (PDB entries: 1E0G  <cite>Bateman2000</cite>, 2MKX and 4PXV). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma et al. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments <cite>Ohnuma2008</cite>. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.
 == Functionalities ==
-CBM50 modules are generally found in bacterial lysins including muramidase [5], N-acetylglucosaminidase [1], -D-glutamate-meso-diaminopimelate muropeptidase [6] and N-acetylmuramoyl-L-alanine amidase [7]. The CBM50 modules in lysins are shown to bind to bacterial peptidoglycan, and involved in cell division by localizing these enzymes to the divisional site [9]. CBM50 modules were also found in family GH18 chitinases [2,8], and contribute to the antifungal activity of the enzymes through their binding ability to chitinous component of the fungal cell wall. CBM50 modules are found not only in carbohydrate-active enzymes but also in LysM-containing plant cell surface receptors for chitin oligosaccharides and their derivatives [10,11] and fungal effectors [12]. The receptor proteins are involved in plant-microbe interactions upon symbiosis and or infection.
+CBM50 modules are generally found in bacterial lysins including muramidase <cite>Chu1992</cite>, ''N''-acetylglucosaminidase <cite>Steen2003</cite>, γ-D-glutamate-meso-diaminopimelate muropeptidase <cite>Margot1999</cite> and ''N''-acetylmuramoyl-L-alanine amidase <cite>Kajimura2005</cite>. The CBM50 modules in lysins are shown to bind to bacterial peptidoglycan, and involved in cell division by localizing these enzymes to the divisional site <cite>Visweswaran2013</cite>. CBM50 modules were also found in family GH18 chitinases <cite>Onaga2008 Gruger2011</cite>, and contribute to the antifungal activity of the enzymes through their binding ability to chitinous component of the fungal cell wall. CBM50 modules are found not only in carbohydrate-active enzymes but also in LysM-containing plant cell surface receptors for chitin oligosaccharides and their derivatives <cite>Kaku2006 Limpens2003</cite> and fungal effectors <cite>Bolton2008</cite>. The receptor proteins are involved in plant-microbe interactions upon symbiosis and or infection.
 == Family Firsts ==
 ;First Identified
-Family 50 CBMs have been known as LysM domains. LysM domain was first identified in the lysozyme from Bacillus phage f29 [13]. LysM domain was first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an N-terminal LysM domain from Pteris ryukyuensis chitinase-A [2,3].
+Family 50 CBMs have been known as LysM domains. LysM domain was first identified in the lysozyme from ''Bacillus phage'' f29 <cite>Garvey1986</cite>. LysM domain was first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an ''N''-terminal LysM domain from ''Pteris ryukyuensis'' chitinase-A Ohnuma2008.
 ;First Structural Characterization
-The first three-dimensional structure of CBM50 module was determined for the LysM domain from E. coli membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: 1E0G) by NMR spectroscopy [4].
+The first three-dimensional structure of CBM50 module was determined for the LysM domain from ''E. coli'' membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: 1E0G) by NMR spectroscopy <cite>Bateman2000</cite>.
 == References ==
@@ Line 40: / Line 40: @@
 #Margot1999 pmid=10206711
 #Kajimura2005 pmid=16262792
 #Gruger2011 pmid=20843785
 #Kaku2006 pmid=16829581
 #Limpens2003 pmid=12947035