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Difference between revisions of "Glycoside Hydrolase Family 127"
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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''' | ||
| Line 18: | Line 17: | ||
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 29: | Line 28: | ||
== Substrate specificities == | == Substrate specificities == | ||
| − | This family of [[glycoside hydrolases]] contains β-L-arabinofuranosidase, which was | + | This family of [[glycoside hydrolases]] contains β-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2014</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin: |
| + | * Ara''f''β1-2Ara''f'' (β-Ara<sub>2</sub>, a product of the [[GH121]] β-L-arabinobiosidase from ''B. longum'' JCM 1217 <cite>Fujita2011A</cite>) | ||
| + | * Ara''f''β-hydroxyproline (Ara-Hyp) | ||
| + | * Ara''f''β1-2Ara''f''β-Hyp (Ara<sub>2</sub>-Hyp) | ||
| + | * Ara''f''β1-2Ara''f''β1-2Ara''f''β-hyp (Ara<sub>3</sub>-Hyp) | ||
| + | * methyl β-L-arabinofuranoside | ||
| + | * Ara''f''β1-2Ara''f''β-Me | ||
| + | |||
| + | The members of GH127 were previosuly known as members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants. Establishment of GH127 by biochemical analysis thus resolved the "domain of unknown function" status of this PFAM family. | ||
| + | |||
| + | ''Note: The original paper describing ''B. longum'' HypBA1 as the founding member of GH127 <cite>Fujita2011B</cite> was withdrawn in 2013 <cite>Fujita2013</cite> and a revised version was published in 2014 <cite>Fujita2014</cite>, to correct errors due to an inadvertent mix-up of sample tubes and data for the E338A and E366A mutants.'' | ||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl β-L-arabinofuranoside was identified by <sup>1</sup>H-NMR and <sup>13</sup>C-NMR analysis <cite>Fujita2014</cite> | |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | In the crystal structure of HypBA1, a Zn<sup>2+</sup> ion was bound to the active site <cite>Ito2014</cite>. A cysteine residue (Cys417), which is involved in the coordination of the Zn<sup>2+</sup>, was suggested to act as the nucleophile. Glu322 is possibly the acid/base catalyst. A possible reaction mechanism involving the cysteine residue as the nucleophile was suggested based on crystal structures, site-directed mutagenesis, some biochemical analysis, and quantum mechanical calculations <cite>Ito2014</cite>. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | HypBA1 from ''B. longum'' JCM 1217 <cite>Ito2014</cite>. It consists of a catalytic (α/α)<sub>6</sub> barrel domain and two additional β-sandwich domains. | |
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: This was determined with HypBA1 enzyme by measurement of glycosyl transfer reactions to methanol and the <sup>1</sup>H-NMR and<sup>13</sup>C-NMR spectra. | + | ;First stereochemistry determination: This was determined with HypBA1 enzyme by measurement of glycosyl transfer reactions to methanol and the <sup>1</sup>H-NMR and<sup>13</sup>C-NMR spectra <cite>Fujita2011B</cite>. |
| − | ;First catalytic nucleophile identification: | + | ;First [[catalytic nucleophile]] identification: |
| − | ;First general acid/base residue identification: | + | ;First [[general acid/base]] residue identification: |
| − | ;First 3-D structure: | + | ;First 3-D structure: HypBA1 from ''B. longum'' JCM 1217 by X-ray crystallography <cite>Ito2014</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | #Fujita2011B | + | #Fujita2011A pmid=21149454 |
| + | #Fujita2011B pmid=21914802 | ||
| + | #Fujita2013 pmid=24143008 | ||
| + | #Fujita2014 pmid=24385433 | ||
| + | #Ito2014 pmid=24680821 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH127]] | [[Category:Glycoside Hydrolase Families|GH127]] | ||
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 GH127 | |
| Clan | none |
| Mechanism | retaining |
| Active site residues | known |
| CAZy DB link | |
| https://www.cazy.org/GH127.html | |
Substrate specificities
This family of glycoside hydrolases contains β-L-arabinofuranosidase activity, which was established for HypBA1 from Bifidobacterium longum JCM 1217 [1]. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
- Arafβ1-2Araf (β-Ara2, a product of the GH121 β-L-arabinobiosidase from B. longum JCM 1217 [2])
- Arafβ-hydroxyproline (Ara-Hyp)
- Arafβ1-2Arafβ-Hyp (Ara2-Hyp)
- Arafβ1-2Arafβ1-2Arafβ-hyp (Ara3-Hyp)
- methyl β-L-arabinofuranoside
- Arafβ1-2Arafβ-Me
The members of GH127 were previosuly known as members of the Pfam DUF1680 family, which is conserved in many species of bacteria, actinomycetes, fungi, and plants. Establishment of GH127 by biochemical analysis thus resolved the "domain of unknown function" status of this PFAM family.
Note: The original paper describing B. longum HypBA1 as the founding member of GH127 [3] was withdrawn in 2013 [4] and a revised version was published in 2014 [1], to correct errors due to an inadvertent mix-up of sample tubes and data for the E338A and E366A mutants.
Kinetics and Mechanism
HypBA1 is a retaining enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl β-L-arabinofuranoside was identified by 1H-NMR and 13C-NMR analysis [1]
Catalytic Residues
In the crystal structure of HypBA1, a Zn2+ ion was bound to the active site [5]. A cysteine residue (Cys417), which is involved in the coordination of the Zn2+, was suggested to act as the nucleophile. Glu322 is possibly the acid/base catalyst. A possible reaction mechanism involving the cysteine residue as the nucleophile was suggested based on crystal structures, site-directed mutagenesis, some biochemical analysis, and quantum mechanical calculations [5].
Three-dimensional structures
HypBA1 from B. longum JCM 1217 [5]. It consists of a catalytic (α/α)6 barrel domain and two additional β-sandwich domains.
Family Firsts
- First stereochemistry determination
- This was determined with HypBA1 enzyme by measurement of glycosyl transfer reactions to methanol and the 1H-NMR and13C-NMR spectra [3].
- First catalytic nucleophile identification
- First general acid/base residue identification
- First 3-D structure
- HypBA1 from B. longum JCM 1217 by X-ray crystallography [5].
References
- Fujita K, Takashi Y, Obuchi E, Kitahara K, and Suganuma T. (2014). Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. J Biol Chem. 2014;289(8):5240-9. DOI:10.1074/jbc.M113.528711 |
- 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 |
- Fujita K, Takashi Y, Obuchi E, Kitahara K, and Suganuma T. (2013). Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum. Functional elucidation of a DUF1680 family member. J Biol Chem. 2013;288(42):30502. DOI:10.1074/jbc.A111.248690 |
- Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, and Fushinobu S. (2014). Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum. Biochem Biophys Res Commun. 2014;447(1):32-7. DOI:10.1016/j.bbrc.2014.03.096 |