Glycoside Hydrolase Family 164 - Revision history

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

2021-12-18T21:19:53Z

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

Harry Brumer: /* Substrate specificities */

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Substrate specificities

Harry Brumer: /* Three-dimensional structures */

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Three-dimensional structures

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reduced figure size on page

Harry Brumer: /* Three-dimensional structures */

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Three-dimensional structures

Harry Brumer: /* Three-dimensional structures */ re-ordered PDB links in text

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Three-dimensional structures: re-ordered PDB links in text

Harry Brumer: Added PDB links in text

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Added PDB links in text

Harry Brumer: /* Three-dimensional structures */

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Three-dimensional structures

Harry Brumer: /* Three-dimensional structures */

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Three-dimensional structures: Removed time-senstive statement.

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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]]: ^^^Zachary Armstrong^^^
+* [[Author]]: [[User:Zachary Armstrong|Zachary Armstrong]]
-* [[Responsible Curator]]:  ^^^Gideon Davies^^^
+* [[Responsible Curator]]:  [[User:Gideon Davies|Gideon Davies]]
 ----

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 [[Image:BS164_AB.png|thumb|right|300px|'''Figure 1. '''The trimeric structure of Bs164 is shown in panel''' A'''. All three protomers are shown with a surface and each chain is displayed as a cartoon diagram coloured by domain.''' B '''shows the structure of one protomer. Domain A, which has a (β/α)8 fold, is shown in green with subdomain H is shown in magenta, domain B, containing a mixed β-sheet, is shown in red and the β-sandwich of domain C is shown in blue. ''See also PDB IDs [{{PDBlink}}6T5O 6T5O], [{{PDBlink}}6T75 6T75], [{{PDBlink}}6T7G 6T7G], and [{{PDBlink}}6T6G 6T6G].'']]
-The defining member of [[glycoside hydrolase]] family 164, a β-mannosidase from ''Bacteroidetes salyersiae'' (''Bs''164, GenbankID: EIY59668.1), was identified initially identified through rational bioinformatic selection of enzyme targets <cite>Helbert2019</cite>. Although ''Bs''164 was initially reported as an α-mannosidase, subsequent detailed biochemical characterization and structure determination revealed that was instead a β-mannosidase <cite>Armstrong2020</cite>. This enzyme is an exo-acting and is capable of cleaving mannooligos and β-mannosides<cite>Armstrong2020</cite>.
+The defining member of [[glycoside hydrolase]] family 164, a β-mannosidase from ''Bacteroides salyersiae'' (''Bs''164, GenbankID: EIY59668.1), was identified initially identified through rational bioinformatic selection of enzyme targets <cite>Helbert2019</cite>. Although ''Bs''164 was initially reported as an α-mannosidase, subsequent detailed biochemical characterization and structure determination revealed that was instead a β-mannosidase <cite>Armstrong2020</cite>. This enzyme is an exo-acting and is capable of cleaving mannooligos and β-mannosides<cite>Armstrong2020</cite>.
 == Kinetics and Mechanism ==

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 == Three-dimensional structures ==
-The structure of ''Bs''164 was solved using multi-wavelength anomalous diffraction of a seleno-methionine labeled protein <cite>Armstrong2020</cite>. The structure of ''Bs''164 has been solved in an uncomplexed state ([{{PDBlink}}6T5O PDB ID 6T5O]), in complex with mannoimidazole ([{{PDBlink}}6T7G PDB ID 6T7G]) and noeuromycin ([{{PDBlink}}6T6G PDB ID 6T6G]), and as a covalent 2-deoxy-2-fluoromannosyl-enzyme intermediate ([{{PDBlink}}6T75 PDB ID 6T75]). Bs164 exists as a donut shaped trimer, see figure 1A. Each trimer-donut has an outer diameter of approximately 100 Å and an internal diameter of between 30 and 35 Å. The individual Bs164 chains contain three clearly defined domains: a modified (β/α)<sub>8</sub> barrel, a domain containing a seven membered mixed β-sheet sandwiched between α-helices, and a β-sheet domain  (Figure 1B). The catalytic residues are present on strands 4 (acid/base) and 7
+The structure of ''Bs''164 was solved using multi-wavelength anomalous diffraction of a seleno-methionine labeled protein <cite>Armstrong2020</cite>. The structure of ''Bs''164 has been solved in an uncomplexed state ([{{PDBlink}}6T5O PDB ID 6T5O]), in complex with mannoimidazole ([{{PDBlink}}6T7G PDB ID 6T7G]) and noeuromycin ([{{PDBlink}}6T6G PDB ID 6T6G]), and as a covalent 2-deoxy-2-fluoromannosyl-enzyme intermediate ([{{PDBlink}}6T75 PDB ID 6T75]). Bs164 exists as a donut shaped trimer (Figure 1A). Each trimer-donut has an outer diameter of approximately 100 Å and an internal diameter of between 30 and 35 Å. The individual Bs164 chains contain three clearly defined domains: a modified (β/α)<sub>8</sub> barrel, a domain containing a seven membered mixed β-sheet sandwiched between α-helices, and a β-sheet domain  (Figure 1B). The catalytic residues are present on strands 4 (acid/base) and 7 (nucleophile) of the (β/α)<sub>8</sub> barrel indicating that GH164 belongs to clan GH-A glycoside hydrolases. This domain architecture is quite similar to that seen for family [[GH42]] enzymes <cite>Hidaka2002</cite>, but is previously unseen for β-mannosidases.
 == Family Firsts ==

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 == Substrate specificities ==
-[[Image:BS164_AB.png|thumb|right|400px|'''Figure 1. '''The trimeric structure of Bs164 is shown in panel''' A'''. All three protomers are shown with a surface and each chain is displayed as a cartoon diagram coloured by domain.''' B '''shows the structure of one protomer. Domain A, which has a (β/α)8 fold, is shown in green with subdomain H is shown in magenta, domain B, containing a mixed β-sheet, is shown in red and the β-sandwich of domain C is shown in blue. ''See also PDB IDs [{{PDBlink}}6T5O 6T5O], [{{PDBlink}}6T75 6T75], [{{PDBlink}}6T7G 6T7G], and [{{PDBlink}}6T6G 6T6G].'']]
+[[Image:BS164_AB.png|thumb|right|300px|'''Figure 1. '''The trimeric structure of Bs164 is shown in panel''' A'''. All three protomers are shown with a surface and each chain is displayed as a cartoon diagram coloured by domain.''' B '''shows the structure of one protomer. Domain A, which has a (β/α)8 fold, is shown in green with subdomain H is shown in magenta, domain B, containing a mixed β-sheet, is shown in red and the β-sandwich of domain C is shown in blue. ''See also PDB IDs [{{PDBlink}}6T5O 6T5O], [{{PDBlink}}6T75 6T75], [{{PDBlink}}6T7G 6T7G], and [{{PDBlink}}6T6G 6T6G].'']]
 The defining member of [[glycoside hydrolase]] family 164, a β-mannosidase from ''Bacteroidetes salyersiae'' (''Bs''164, GenbankID: EIY59668.1), was identified initially identified through rational bioinformatic selection of enzyme targets <cite>Helbert2019</cite>. Although ''Bs''164 was initially reported as an α-mannosidase, subsequent detailed biochemical characterization and structure determination revealed that was instead a β-mannosidase <cite>Armstrong2020</cite>. This enzyme is an exo-acting and is capable of cleaving mannooligos and β-mannosides<cite>Armstrong2020</cite>.

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 == Three-dimensional structures ==
-The structure of ''Bs''164 was solved using multi-wavelength anomalous diffraction of a seleno-methionine labeled protein <cite>Armstrong2020</cite>. The structure of ''Bs''164 has been solved in an uncomplexed state ([{{PDBlink}}6T5O PDB ID 6T5O]) and in complex with mannoimidazole ([{{PDBlink}}6T7G PDB ID 6T7G]), noeuromycin ([{{PDBlink}}6T6G PDB ID 6T6G]), and 2-deoxy-2-fluoromannose ([{{PDBlink}}6T75 PDB ID 6T75]). Bs164 exists as a donut shaped trimer, see figure 1A. Each trimer-donut has an outer diameter of approximately 100 Å and an internal diameter of between 30 and 35 Å. The individual Bs164 chains contain three clearly defined domains: a modified (β/α)<sub>8</sub> barrel, a domain containing a seven membered mixed β-sheet sandwiched between α-helices, and a β-sheet domain  (Figure 1B). The catalytic residues are present on strands 4 (acid/base) and 7
+The structure of ''Bs''164 was solved using multi-wavelength anomalous diffraction of a seleno-methionine labeled protein <cite>Armstrong2020</cite>. The structure of ''Bs''164 has been solved in an uncomplexed state ([{{PDBlink}}6T5O PDB ID 6T5O]), in complex with mannoimidazole ([{{PDBlink}}6T7G PDB ID 6T7G]) and noeuromycin ([{{PDBlink}}6T6G PDB ID 6T6G]), and as a covalent 2-deoxy-2-fluoromannosyl-enzyme intermediate ([{{PDBlink}}6T75 PDB ID 6T75]). Bs164 exists as a donut shaped trimer, see figure 1A. Each trimer-donut has an outer diameter of approximately 100 Å and an internal diameter of between 30 and 35 Å. The individual Bs164 chains contain three clearly defined domains: a modified (β/α)<sub>8</sub> barrel, a domain containing a seven membered mixed β-sheet sandwiched between α-helices, and a β-sheet domain  (Figure 1B). The catalytic residues are present on strands 4 (acid/base) and 7
 (nucleophile) of the (β/α)<sub>8</sub> barrel indicating that GH164 belongs to clan GH-A glycoside hydrolases. This domain architecture is quite similar to that seen for family [[GH42]] enzymes <cite>Hidaka2002</cite>, but is previously unseen for β-mannosidases.