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Difference between revisions of "Glycoside Hydrolase Family 145"

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{{CuratorApproved}}
 
* [[Author]]: ^^^Alan Cartmell^^^
 
* [[Author]]: ^^^Alan Cartmell^^^
* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
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* [[Responsible Curator]]:  ^^^Alan Cartmell^^^
 
----
 
----
  
 
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
 
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
 
<div style="float:right">
 
<div style="float:right">
{| {{Prettytable}}  
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{| {{Prettytable}}
 
|-
 
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''
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| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''
 
|-
 
|-
|'''Clan'''  
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| '''Clan'''
|GH-x
+
| None
 
|-
 
|-
|'''Mechanism'''
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| '''Mechanism'''
|retaining/inverting
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| retaining
 
|-
 
|-
|'''Active site residues'''
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| '''Active site residues'''
|known/not known
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| known
 
|-
 
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
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| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|-
 
|-
 
| colspan="2" |{{CAZyDBlink}}GH145.html
 
| colspan="2" |{{CAZyDBlink}}GH145.html
 
|}
 
|}
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</div>
 
</div>
 +
 
<!-- This is the end of the table -->
 
<!-- This is the end of the table -->
 
 
 
== Substrate specificities ==
 
== Substrate specificities ==
Content is to be added here.
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Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>.  
 
 
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''
 
 
 
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.
 
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
Content is to be added here.
+
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates.  
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
Content is to be added here.
+
A single catalytic histidine, His48 in BT3686, has been shown to be critical for activity. This was the only residue mutated (to Gln, Ala and Gly) that caused loss of activity and is thought to act as an acid/base. Several homologues of BT3686 exist, which although >80 % identical are inactive due to having Gln at the equivalent position to His48 in BT3686. The introduction of a histidine at into related enzymes BACINT_00347 and BACCELL_00856, from ''Bacteroides intestinalis'' and ''Bacteroides cellulosilyticus'', generating the mutants Q48H in both proteins, is sufficient to introduce rhamnosidase activity into these, otherwise inactive, enzymes <cite>Munoz-Munoz2017</cite>. No second catalytic residue to could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, portonating its own O4 and activating a water molecule.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
Content is to be added here.
+
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.
  
 
== Family Firsts ==
 
== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
+
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.
;First catalytic nucleophile identification: Content is to be added here.
+
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.
;First general acid/base residue identification: Content is to be added here.
+
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.
;First 3-D structure: Content is to be added here.
+
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively.  <cite>Munoz-Munoz2017</cite>.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#Cantarel2009 pmid=18838391
+
#Munoz-Munoz2017 pmid=28396425
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+
#Cartmell2019 pmid=31541200
 +
#Thompson2012 pmid=22219371
 +
#Fernandes2018 pmid=29508463
 +
#Ulaganathan2017 pmid=28290654
 
</biblio>
 
</biblio>
 +
  
 
[[Category:Glycoside Hydrolase Families|GH145]]
 
[[Category:Glycoside Hydrolase Families|GH145]]

Latest revision as of 08:20, 12 May 2020

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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 GH145
Clan None
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/GH145.html

Substrate specificities

Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic [1, 2].

Kinetics and Mechanism

NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism [1]. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes [3, 4]. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage [1]. Further work is needed to confirm the mechanism by which GH145 operates.

Catalytic Residues

A single catalytic histidine, His48 in BT3686, has been shown to be critical for activity. This was the only residue mutated (to Gln, Ala and Gly) that caused loss of activity and is thought to act as an acid/base. Several homologues of BT3686 exist, which although >80 % identical are inactive due to having Gln at the equivalent position to His48 in BT3686. The introduction of a histidine at into related enzymes BACINT_00347 and BACCELL_00856, from Bacteroides intestinalis and Bacteroides cellulosilyticus, generating the mutants Q48H in both proteins, is sufficient to introduce rhamnosidase activity into these, otherwise inactive, enzymes [1]. No second catalytic residue to could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, portonating its own O4 and activating a water molecule.

Three-dimensional structures

GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity [1, 5].

Family Firsts

First stereochemistry determination
Determined for the bacteroides thetaiotaomicron enzyme BT3686 [1].
First catalytic acid/base residue identification
Predicted to be a histidine [1].
Second general acid/base residue identification
Predicted to be provided by the substrate [1].
First 3-D structure
BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms bacteroides thetaiotaomicron, bacteroides intestinalis and bacteroides cellulosilyticus, respectively. [1].

References

  1. Munoz-Munoz J, Cartmell A, Terrapon N, Henrissat B, and Gilbert HJ. (2017) Unusual active site location and catalytic apparatus in a glycoside hydrolase family. Proc Natl Acad Sci U S A. 114, 4936-4941. DOI:10.1073/pnas.1701130114 | PubMed ID:28396425 | HubMed [Munoz-Munoz2017]
  2. Cartmell A, Muñoz-Muñoz J, Briggs JA, Ndeh DA, Lowe EC, Baslé A, Terrapon N, Stott K, Heunis T, Gray J, Yu L, Dupree P, Fernandes PZ, Shah S, Williams SJ, Labourel A, Trost M, Henrissat B, and Gilbert HJ. (2019) Author Correction: A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation. Nat Microbiol. 4, 2021-2023. DOI:10.1038/s41564-019-0584-5 | PubMed ID:31541200 | HubMed [Cartmell2019]
  3. Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stütz AE, Butters TD, Williams SJ, and Davies GJ. (2012) Structural and mechanistic insight into N-glycan processing by endo-α-mannosidase. Proc Natl Acad Sci U S A. 109, 781-6. DOI:10.1073/pnas.1111482109 | PubMed ID:22219371 | HubMed [Thompson2012]
  4. Fernandes PZ, Petricevic M, Sobala L, Davies GJ, and Williams SJ. (2018) Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. Chemistry. 24, 7464-7473. DOI:10.1002/chem.201800435 | PubMed ID:29508463 | HubMed [Fernandes2018]
  5. Ulaganathan T, Boniecki MT, Foran E, Buravenkov V, Mizrachi N, Banin E, Helbert W, and Cygler M. (2017) New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. ACS Chem Biol. 12, 1269-1280. DOI:10.1021/acschembio.7b00126 | PubMed ID:28290654 | HubMed [Ulaganathan2017]
All Medline abstracts: PubMed | HubMed