Glycoside Hydrolase Family 105

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• Author: ^^^James Stevenson^^^
• Responsible Curator: ^^^Joel Weadge^^^

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Glycoside Hydrolase Family GH105
Clan	GH-x
Mechanism	retaining/inverting
Active site residues	known/not known
CAZy DB link
https://www.cazy.org/GH105.html

Substrate specificities

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated [1]. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates [2, 3]. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes [2, 4]. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins [2, 5, 6, 7].

Kinetics and Mechanism

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism [8], rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate [5]. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure [6], but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family [3, 9]

Catalytic Residues

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Three-dimensional structures

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Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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References

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1. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |

8. Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. Biological Reviews, vol. 28, no. 4., pp. 416-436. [1].

12. JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. RCSB Protein Data Bank. [1].

13. Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. RCSB Protein Data Bank. [1].

15. Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. RCSB Protein Data Bank. [1].

16. Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. RCSB Protein Data Bank. [1].

17. Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. RCSB Protein Data Bank. [1].