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Difference between revisions of "Glycoside Hydrolase Family 124"
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| − | * [[Author]]: | + | * [[Author]]: [[User:Harry Gilbert|Harry Gilbert]] |
| − | * [[Responsible Curator]]: | + | * [[Responsible Curator]]: [[User:Harry Gilbert|Harry Gilbert]] |
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|- | |- | ||
|'''Clan''' | |'''Clan''' | ||
| − | | | + | |None |
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
| − | | | + | |Inverting |
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |Catalytic acid known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 29: | Line 29: | ||
== Substrate specificities == | == Substrate specificities == | ||
| − | Family | + | Family GH124 consists of a small number of celluloytic [[glycoside hydrolases]]. The ''Clostridium thermocellum'' enzyme ''Ct''Cel124A is the only member of this family that has been characterized. The enzyme is an ''[[endo]]''-β1,4-glucanase with modest activity ''in vitro'', but acts in synergy with the major ''[[exo]]''-cellulase from ''C. thermocellum'' and, as a discrete entity, is able to deconstruct tobacco cell walls <cite>Bras2011</cite>. |
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | Using cellopentaose as the substrate and HPLC the enzyme was shown to utilize a single displacement, [[inverting]] mechanism <cite>Bras2011</cite>. | |
| − | |||
| − | |||
== Catalytic Residues == | == Catalytic Residues == | ||
| − | The catalytic acid in ''Ct''Cel124A was shown to be Glu96 based on the crystal structural of the enzyme and the observation that the | + | The catalytic [[general acid]] in ''Ct''Cel124A was shown to be Glu96 based on the crystal structural of the enzyme and the observation that the E96A mutation completely inactivates the cellulase <cite>Bras2011</cite>. The enzyme contains no candidate catalytic [[general base]] and it was suggested that the nucleophilic water was activated by a "Grotthus-like" mechanism, as previously proposed for some [[GH6]] cellulases <cite>Koivula2002</cite>. |
| − | |||
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | The enzyme displays a superhelical fold in which a constellation of α-helices | + | The enzyme displays a superhelical fold in which a constellation of α-helices encircling a central helix that houses the catalytic apparatus. This fold was described as having closest similarity to black swan lysozyme G (Lyz23) from family [[GH23]] <cite>Bras2011</cite>; similarities also exist to family [[GH19]] chitinases, family [[GH22]] lysozymes, and family [[GH134]] β-mannanases. The catalytic acid, Glu96, is located at the C-terminus of the central helix. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose. The active site of ''Ct''Cel124 displays remarkable structural conservation with a [[GH23]] lytic transglycosylase <cite>Bras2011</cite>. |
| − | suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose . | ||
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: | + | ;First stereochemistry determination: The sterochemical outcome of catalysis is [[inverting|inversion]] of the β linkage into the α anomer <cite>Bras2011</cite>. The method used to detect the stereochemical outcome was the HPLC method of Braun et al. <cite>Braun1993</cite>. The reaction was too slow to detect through NMR as rapid mutarotation obscured the sterochemistry of glycosidic bond cleavage. |
| − | + | ;First [[general base]] residue identification: The candidate catalytic base has not been identified. | |
| − | ;First general acid/base residue identification: | + | ;First [[general acid/base]] residue identification: The catalytic [[general acid]] was identified from analysis of structure in harness with mutagenesis data and sequence analysis <cite>Bras2011</cite>. |
| − | ;First 3-D structure: | + | ;First 3-D structure: The X-ray crystal structure of ''Ct''Cel124 was determined in complex with two cellotriose molecules. The structure revealed a novel cellulase fold and hinted that the enzyme attacks cellulose at the interface between two structural domains of the substrate <cite>Bras2011</cite>. |
== References == | == References == | ||
| Line 55: | Line 50: | ||
#Bras2011 pmid=21393568 | #Bras2011 pmid=21393568 | ||
#Koivula2002 pmid=12188666 | #Koivula2002 pmid=12188666 | ||
| − | # | + | #Braun1993 pmid=8368500 |
| − | |||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH124]] | [[Category:Glycoside Hydrolase Families|GH124]] | ||
Latest revision as of 13:18, 18 December 2021
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| Glycoside Hydrolase Family GH124 | |
| Clan | None |
| Mechanism | Inverting |
| Active site residues | Catalytic acid known |
| CAZy DB link | |
| https://www.cazy.org/GH124.html | |
Substrate specificities
Family GH124 consists of a small number of celluloytic glycoside hydrolases. The Clostridium thermocellum enzyme CtCel124A is the only member of this family that has been characterized. The enzyme is an endo-β1,4-glucanase with modest activity in vitro, but acts in synergy with the major exo-cellulase from C. thermocellum and, as a discrete entity, is able to deconstruct tobacco cell walls [1].
Kinetics and Mechanism
Using cellopentaose as the substrate and HPLC the enzyme was shown to utilize a single displacement, inverting mechanism [1].
Catalytic Residues
The catalytic general acid in CtCel124A was shown to be Glu96 based on the crystal structural of the enzyme and the observation that the E96A mutation completely inactivates the cellulase [1]. The enzyme contains no candidate catalytic general base and it was suggested that the nucleophilic water was activated by a "Grotthus-like" mechanism, as previously proposed for some GH6 cellulases [2].
Three-dimensional structures
The enzyme displays a superhelical fold in which a constellation of α-helices encircling a central helix that houses the catalytic apparatus. This fold was described as having closest similarity to black swan lysozyme G (Lyz23) from family GH23 [1]; similarities also exist to family GH19 chitinases, family GH22 lysozymes, and family GH134 β-mannanases. The catalytic acid, Glu96, is located at the C-terminus of the central helix. The substrate-binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively, suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose. The active site of CtCel124 displays remarkable structural conservation with a GH23 lytic transglycosylase [1].
Family Firsts
- First stereochemistry determination
- The sterochemical outcome of catalysis is inversion of the β linkage into the α anomer [1]. The method used to detect the stereochemical outcome was the HPLC method of Braun et al. [3]. The reaction was too slow to detect through NMR as rapid mutarotation obscured the sterochemistry of glycosidic bond cleavage.
- First general base residue identification
- The candidate catalytic base has not been identified.
- First general acid/base residue identification
- The catalytic general acid was identified from analysis of structure in harness with mutagenesis data and sequence analysis [1].
- First 3-D structure
- The X-ray crystal structure of CtCel124 was determined in complex with two cellotriose molecules. The structure revealed a novel cellulase fold and hinted that the enzyme attacks cellulose at the interface between two structural domains of the substrate [1].
References
- Brás JL, Cartmell A, Carvalho AL, Verzé G, Bayer EA, Vazana Y, Correia MA, Prates JA, Ratnaparkhe S, Boraston AB, Romão MJ, Fontes CM, and Gilbert HJ. (2011). Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. Proc Natl Acad Sci U S A. 2011;108(13):5237-42. DOI:10.1073/pnas.1015006108 |
- Koivula A, Ruohonen L, Wohlfahrt G, Reinikainen T, Teeri TT, Piens K, Claeyssens M, Weber M, Vasella A, Becker D, Sinnott ML, Zou JY, Kleywegt GJ, Szardenings M, Ståhlberg J, and Jones TA. (2002). The active site of cellobiohydrolase Cel6A from Trichoderma reesei: the roles of aspartic acids D221 and D175. J Am Chem Soc. 2002;124(34):10015-24. DOI:10.1021/ja012659q |
- Braun C, Meinke A, Ziser L, and Withers SG. (1993). Simultaneous high-performance liquid chromatographic determination of both the cleavage pattern and the stereochemical outcome of the hydrolysis reactions catalyzed by various glycosidases. Anal Biochem. 1993;212(1):259-62. DOI:10.1006/abio.1993.1320 |