Carbohydrate Binding Module Family 67 - Revision history

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

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

Harry Brumer at 16:33, 16 November 2018

2018-11-16T16:33:59Z

Harry Brumer: changed figure placement on page

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Elizabeth Ficko-Blean at 09:42, 16 November 2018

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Elizabeth Ficko-Blean at 09:41, 16 November 2018

2018-11-16T09:41:38Z

Elizabeth Ficko-Blean at 09:38, 16 November 2018

2018-11-16T09:38:37Z

Elizabeth Ficko-Blean at 09:36, 16 November 2018

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Satoshi Kaneko at 01:19, 16 November 2018

2018-11-16T01:19:14Z

Satoshi Kaneko at 07:07, 15 November 2018

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Satoshi Kaneko at 07:00, 15 November 2018

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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]]: ^^^Satoshi Kaneko^^^
+* [[Author]]: [[User:Satoshi Kaneko|Satoshi Kaneko]]
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
+* [[Responsible Curator]]:  [[User:Harry Gilbert|Harry Gilbert]]
 ----

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 == Structural Features ==
-[[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.'''  The structure of ʟ-rhamnose binding pocket of SaCBM67  [{{PDBlink}}3w5n 3W5N].]]
+[[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.'''  The structure of ʟ-rhamnose binding pocket of SaCBM67 (PDB ID [{{PDBlink}}3w5n 3W5N]).]]
 SaCBM67 is a ʟ-rhamnose binding module. The exo-binding manner with the shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, and C) <cite>Fujimoto2013</cite>. Domain D is designated as SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
 == Functionalities ==
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 </biblio>
-[[Category:Carbohydrate Binding Module Families|CBM067]] <!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. -->
+[[Category:Carbohydrate Binding Module Families|CBM067]]

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 == Structural Features ==
 [[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.'''  The structure of ʟ-rhamnose binding pocket of SaCBM67  [{{PDBlink}}3w5n 3W5N].]]
+SaCBM67 is a ʟ-rhamnose binding module. The exo-binding manner with the shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, and C) <cite>Fujimoto2013</cite>. Domain D is designated as SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
 == Functionalities ==
 SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. The D179A and N180A mutant enzymes lost their binding ability to ʟ-rhamnose which caused a substantial reduction (∼50-fold) in activity against ʟ-rhamnose-containing polysaccharides, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.

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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]]: ^^^Satoshi Kaneko^^^
 * [[Responsible Curator]]:  ^^^Harry Gilbert^^^

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 == Structural Features ==
-SaCBM67 is a ʟ-rhamnose binding module. The exo-binding manner with the shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D is designated as SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
+SaCBM67 is a ʟ-rhamnose binding module. The exo-binding manner with the shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, and C)<cite>Fujimoto2013</cite>. Domain D is designated as SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
 [[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.'''  The structure of ʟ-rhamnose binding pocket of SaCBM67  [{{PDBlink}}3w5n 3W5N].]]

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 == Family Firsts ==
-;First Identified
+;First Identified: SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
-:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
+;First Structural Characterization: The first structure of CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a characterized member of CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.
 == References ==

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 == Ligand specificities ==
-The sugar binding structure of a [[GH78]] α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but it did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly, the D179A and N180A mutants of SaCBM67, in which removed hydrogen bonds with calcium, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was observed <cite>Fujimoto2013</cite>.
+The sugar binding structure of a [[GH78]] α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but it did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly, the D179A and N180A mutants of SaCBM67, in which removed hydrogen bonds with calcium abolish ligand binding, confirm the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was observed <cite>Fujimoto2013</cite>.
 == Structural Features ==
-SaCBM67 is a ʟ-rhamnose binding module. The exo binding manner with shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D designated SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
+SaCBM67 is a ʟ-rhamnose binding module. The exo-binding manner with the shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D is designated as SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.
 [[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.'''  The structure of ʟ-rhamnose binding pocket of SaCBM67  [{{PDBlink}}3w5n 3W5N].]]
 == Functionalities ==
-Although SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually D179A and N180A mutant enzymes losted binding ability to ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.
+SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. The D179A and N180A mutant enzymes lost their binding ability to ʟ-rhamnose which caused a substantial reduction (∼50-fold) in activity against ʟ-rhamnose-containing polysaccharides, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.
 CBM67 members are distributed not only in many bacterial [[GH78]] α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree<cite>Fujimoto2013</cite>. Although the calcium binding site is conserved in CBM67 members, these CBM67 members might show different sugar specificities because the ʟ-rhamnose binding residues in SaCBM67 are not retained in all the subfamilies. For example, the lectin from ''Pleurotus cornucopiae'', containing two CBM67-like sequences in tandem with sequence identities with SaCBM67 of 25 and 35% for the N- and C-terminal modules, respectively, shows the highest affinity for ''N''-acetyl-ᴅ-galactosamine<cite>Fujimoto2013</cite>.