Glycoside Hydrolase Family 141

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• Author: Ana Luis
• Responsible Curator: Harry Gilbert

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Glycoside Hydrolase Family GH141
Clan	none
Mechanism	unknown
Active site residues	known
CAZy DB link
https://www.cazy.org/GH141.html

Substrate specificities

Glycoside hydrolases of family 141 display α-L-fucosidase (EC 3.2.1.51) [1] or xylanase (EC 3.2.1.8) [2] activities. The Bacteroides thetaiotaomicron enzyme BT1002 is the founding member of this family. This enzyme cleaves the fucosodic linkage in 2-O-methyl-D-xylosyl-α-1,3-L-fucosyl-α1,4-L-Rhap, a component of chain B of rhamnogalacturonan II, a complex pectin conserved in the primary cell walls of plants [1]. Recently, an endo-xylanase from Clostridium thermocellum (Xyn141E) was also described. Xyn141E is active against a range of xylans, displaying low level activity against other β1,4-glycans such as carboxymethyl cellulose, barley beta glucan and ivory nut mannan [2].

Kinetics and Mechanism

Very little is known about the kinetics or mechanism of family 141 enzymes. However, in the BT1002 crystal structure, the distance of 6.1 Å between the catalytic residues suggests that members of this family may be retaining enzymes and follow a double displacement mechanism [1].

Catalytic Residues

In the X-ray crystal structure of B. thetaiotaomicron BT1002, two aspartates (Asp523 and Asp564), which are highly conserved and located within the active site pocket, are the proposed catalytic residues. Site directed mutagenesis of these amino acids abolished the catalytic activity of BT1002 indicating the essential role in catalysis. Additionally, the structural location of the catalytic residues suggests that Asp523 (at the base of the pocket) acts as catalytic nucleophile and Asp564 (at the lip of the active site) is the general acid-base residue [1].

Three-dimensional structures

Figure 1. BT1002 strucutre. (PDB ID 5PDB) The figure shows the β-parallel catalytic domain (purple) and the additional β-sandwich domain (yellow)

The three-dimensional structure has been determined for B. thetaiotaomicron BT1002 at 2 Å (PDB ID 5PDB). The protein has two domains: a N-terminal β-sandwich and a C-terminal catalytic domain that folds into a right-handed parallel β-helix . The overall fold displays similarity to members of Polysaccharide Lyase Family 1 and Glycoside Hydrolase Family 28 (Figure 1) [1]. The active site pocket is in a similar location to the catalytic centre of GH120 β-xylosidases [3], which also displays the same fold as the GH141 enzyme BT1002. The catalytic resisdues identified in the GH120 β-xylosidase [4], however, are not conserved in the GH141 α-L-fucosidase.

Family Firsts

First stereochemistry determination

Currently unknown.

First catalytic nucleophile identification

BT1002 from Bacteroides thetaiotaomicron [1].

First general acid/base residue identification

BT1002 from Bacteroides thetaiotaomicron [1].

First 3-D structure

BT1002 from Bacteroides thetaiotaomicron [1].

References

1. Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, and Gilbert HJ. (2017). Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature. 2017;544(7648):65-70. DOI:10.1038/nature21725 |
2. Heinze S, Mechelke M, Kornberger P, Liebl W, Schwarz WH, and Zverlov VV. (2017). Identification of endoxylanase XynE from Clostridium thermocellum as the first xylanase of glycoside hydrolase family GH141. Sci Rep. 2017;7(1):11178. DOI:10.1038/s41598-017-11598-y |
3. Huang CH, Sun Y, Ko TP, Chen CC, Zheng Y, Chan HC, Pang X, Wiegel J, Shao W, and Guo RT. (2012). The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485. Biochem J. 2012;448(3):401-7. DOI:10.1042/BJ20121359 |
4. Cecchini DA, Fauré R, Laville E, and Potocki-Veronese G. (2015). Biochemical identification of the catalytic residues of a glycoside hydrolase family 120 β-xylosidase, involved in xylooligosaccharide metabolisation by gut bacteria. FEBS Lett. 2015;589(20 Pt B):3098-106. DOI:10.1016/j.febslet.2015.08.012 |