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Difference between revisions of "Glycoside Hydrolase Family 121"
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| − | + | {{CuratorApproved}} | |
| − | + | * [[Author]]: [[User:Kiyotaka Fujita|Kiyotaka Fujita]] | |
| − | * [[Author]]: | + | * [[Responsible Curator]]: [[User:Shinya Fushinobu|Shinya Fushinobu]] |
| − | * [[Responsible Curator]]: | ||
---- | ---- | ||
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|- | |- | ||
|'''Clan''' | |'''Clan''' | ||
| − | | | + | |none |
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
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|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |not known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
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</div> | </div> | ||
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== Substrate specificities == | == Substrate specificities == | ||
| − | This family of glycoside hydrolases | + | This family of [[glycoside hydrolases]] contains β-L-arabinobiosidases, as demonstrated for HypBA2 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011A</cite>. HypBA2 liberates the disaccharide Ara''f''β1-2Ara''f'' (β-Ara<sub>2</sub>, a substrate of the [[GH127]] β-L-arabinofuranosidase from ''B. longum'' JCM 1217 <cite>Fujita2011B</cite>) from unmodified Ara''f''β1-2Ara''f''β1-2Ara''f''β-hydroxyproline (Ara<sub>3</sub>-Hyp), but not Ara''f''α1-3Ara''f''β1-2Ara''f''β1-2Ara''f''β-Hyp (Ara<sub>4</sub>-Hyp) or Ara''f''β1-2Ara''f''β-Hyp (Ara<sub>2</sub>-Hyp). HypBA2 directly liberates β-Ara<sub>2</sub> from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes. |
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | HypBA2 is a retaining enzyme. | + | HypBA2 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Ara''f''β1-2Ara''f''β-Me was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2011A</cite>. |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | The catalytic residues are not known but three conserved residues (Glu373, Asp515, and Glu713 in ''B. longum'' HypBA2) are the candidates based on mutagenesis and structural comparison <cite>Saito2020</cite>. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | [[File:GH121-HypBA2.png|thumb|300px|right|'''Figure 1:''' β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum''. The catalytic (α/α)<sub>6</sub> barrel domain is in green.]] | |
| + | The first solved 3-D structure was β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' (PDB [{{PDBlink}}6m5a 6M5A]) <cite>Saito2020</cite>. The catalytic domain adops an (α/α)<sub>6</sub> barrel fold similar to [[GH142]], [[GH63]], [[GH78]], [[GH94]], and [[GH37]] ('''Figure 1'''). | ||
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: | + | ;First stereochemistry determination: Shown to be [[retaining]] for HypBA2 by product analysis of glycosyl transfer reactions to methanol <cite>Fujita2011A</cite>. |
| + | ;First catalytic nucleophile identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof. | ||
| + | ;First general acid/base residue identification: Predicted based on structural homology <cite>Saito2020</cite>, but currently no experimental proof. | ||
| + | ;First 3-D structure: β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' <cite>Saito2020</cite>. | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Fujita2011A pmid=21149454 |
| − | # | + | #Fujita2011B pmid=21914802 |
| + | #Saito2020 pmid=32479540 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH121]] | [[Category:Glycoside Hydrolase Families|GH121]] | ||
Latest revision as of 13:18, 18 December 2021
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
| Glycoside Hydrolase Family GH121 | |
| Clan | none |
| Mechanism | retaining |
| Active site residues | not known |
| CAZy DB link | |
| https://www.cazy.org/GH121.html | |
Substrate specificities
This family of glycoside hydrolases contains β-L-arabinobiosidases, as demonstrated for HypBA2 from Bifidobacterium longum JCM 1217 [1]. HypBA2 liberates the disaccharide Arafβ1-2Araf (β-Ara2, a substrate of the GH127 β-L-arabinofuranosidase from B. longum JCM 1217 [2]) from unmodified Arafβ1-2Arafβ1-2Arafβ-hydroxyproline (Ara3-Hyp), but not Arafα1-3Arafβ1-2Arafβ1-2Arafβ-Hyp (Ara4-Hyp) or Arafβ1-2Arafβ-Hyp (Ara2-Hyp). HypBA2 directly liberates β-Ara2 from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes.
Kinetics and Mechanism
HypBA2 is a retaining enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Arafβ1-2Arafβ-Me was identified by 1H-NMR and 13C-NMR analysis [1].
Catalytic Residues
The catalytic residues are not known but three conserved residues (Glu373, Asp515, and Glu713 in B. longum HypBA2) are the candidates based on mutagenesis and structural comparison [3].
Three-dimensional structures
The first solved 3-D structure was β-L-arabinobiosidase HypBA2 from Bifidobacterium longum (PDB 6M5A) [3]. The catalytic domain adops an (α/α)6 barrel fold similar to GH142, GH63, GH78, GH94, and GH37 (Figure 1).
Family Firsts
- First stereochemistry determination
- Shown to be retaining for HypBA2 by product analysis of glycosyl transfer reactions to methanol [1].
- First catalytic nucleophile identification
- Predicted based on structural homology [3], but currently no experimental proof.
- First general acid/base residue identification
- Predicted based on structural homology [3], but currently no experimental proof.
- First 3-D structure
- β-L-arabinobiosidase HypBA2 from Bifidobacterium longum [3].
References
- Fujita K, Sakamoto S, Ono Y, Wakao M, Suda Y, Kitahara K, and Suganuma T. (2011). Molecular cloning and characterization of a beta-L-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J Biol Chem. 2011;286(7):5143-50. DOI:10.1074/jbc.M110.190512 |
- Fujita K, Takashi Y, Obuchi E, Kitahara K, and Suganuma T. (2011). Characterization of a novel β-L-Arabinofuranosidase in Bifidobacterium longum: functional elucidation of A DUF1680 family member. J Biol Chem. 2011;286(44):38079-38085. DOI:10.1074/jbc.M111.248690 |
- Saito K, Viborg AH, Sakamoto S, Arakawa T, Yamada C, Fujita K, and Fushinobu S. (2020). Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121. PLoS One. 2020;15(6):e0231513. DOI:10.1371/journal.pone.0231513 |