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Difference between revisions of "Glycoside Hydrolase Family 145"

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* [[Author]]: [[User:Harry Brumer|Harry Brumer]]
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* [[Author]]: ^^^Alan Cartmell^^^
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* [[Responsible Curator]]: [[User:Bernard Henrissat|Bernard Henrissat]]
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* [[Responsible Curator]]: ^^^Harry Gilbert^^^
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=== GH145 is a deleted family ===
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This family has been reclassified as [[Polysaccharide Lyase Family 42]]. Two members of the family from ''Bacteroides'' species were originally shown to have hydrolase activity catalyzed by a semi-conserved active site on the posterior side of the beta-propeller structure <cite>MunozMunoz2017</cite>.  Subsequently, lyase activity on alpha-L-Rha-1,4-alpha-D-GlcA via a well-conserved active site on the anterior surface, with strong similarity to [[PL24]] and [[PL25]], was demonstrated in fungal <cite>Kondo2021</cite> and bacterial <cite>MunozMunoz2021</cite>  homologs.
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'''References'''
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<biblio>
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#MunozMunoz2017 pmid=28396425
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#MunozMunoz2021 pmid=34340552
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#Kondo2021 pmid=34303708
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</biblio>
 
<!-- 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 -->
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{| {{Prettytable}}  
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{| {{Prettytable}}
 
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|-
 
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| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''
 
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| '''Clan'''
 
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| GH-x
 
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| '''Mechanism'''
 
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| retaining
 
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| '''Active site residues'''
 
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| known
 
 
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| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB links'''
 
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| colspan="2" |{{CAZyDBlink}}GH145.html
 
| colspan="2" |{{CAZyDBlink}}GH145.html
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</div>
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|-
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| colspan="2" |{{CAZyDBlink}}PL42.html
  
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|}
 
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== Substrate specificities ==
 
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Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>.
 
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== Kinetics and Mechanism ==
 
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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>Thompson=2012 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.
 
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== Catalytic Residues ==
 
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A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.
 
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== Three-dimensional structures ==
 
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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>.
 
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== Family Firsts ==
 
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;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686
 
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;First catalytic acid/base residue identification: Predicted to be a histidine
 
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;Second general acid/base residue identification: Predicted to be provided by the substrate.
 
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;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.
 
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== References ==
 
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<references/><biblio>
 
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#Munoz-Munoz2017 pmid=28396425
 
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#Cartmell2019 pmid=31541200
 
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#Thompson2012 pmid=22219371
 
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#Fernandes2018 pmid=29508463
 
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#Ulaganathan2017 pmid=28290654
 
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#Cantarel2009 pmid=18838391
 
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#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].
 
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[[Category:Glycoside Hydrolase Families|GH145]]
 
[[Category:Glycoside Hydrolase Families|GH145]]

Latest revision as of 14:15, 18 December 2021

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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.

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This family has been deleted from the CAZy classification. A specific explanation may be found below.

GH145 is a deleted family

This family has been reclassified as Polysaccharide Lyase Family 42. Two members of the family from Bacteroides species were originally shown to have hydrolase activity catalyzed by a semi-conserved active site on the posterior side of the beta-propeller structure [1]. Subsequently, lyase activity on alpha-L-Rha-1,4-alpha-D-GlcA via a well-conserved active site on the anterior surface, with strong similarity to PL24 and PL25, was demonstrated in fungal [2] and bacterial [3] homologs.

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. 2017;114(19):4936-4941. DOI:10.1073/pnas.1701130114 | PubMed ID:28396425 [MunozMunoz2017]
  2. Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, and Sakamoto T. (2021). Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem. 2021;297(3):101001. DOI:10.1016/j.jbc.2021.101001 | PubMed ID:34303708 [Kondo2021]
  3. Munoz-Munoz J, Ndeh D, Fernandez-Julia P, Walton G, Henrissat B, and Gilbert HJ. (2021). Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius. mBio. 2021;12(4):e0136821. DOI:10.1128/mBio.01368-21 | PubMed ID:34340552 [MunozMunoz2021]

All Medline abstracts: PubMed

CAZy DB links
http://www.cazy.org/GH145.html
http://www.cazy.org/PL42.html
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