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

2. Munoz-Munoz J, Cartmell A, Terrapon N, Baslé A, Henrissat B, and Gilbert HJ. (2017). An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. J Biol Chem. 2017;292(32):13271-13283. DOI:10.1074/jbc.M117.794578 |
4. Zhang R, Minh T, Lezondra L, Korolev S, Moy SF, Collart F, and Joachimiak A. (2005). 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins. 2005;60(3):561-5. DOI:10.1002/prot.20410 |
5. Itoh T, Ochiai A, Mikami B, Hashimoto W, and Murata K. (2006). Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem Biophys Res Commun. 2006;347(4):1021-9. DOI:10.1016/j.bbrc.2006.07.034 |
6. Itoh T, Ochiai A, Mikami B, Hashimoto W, and Murata K. (2006). A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J Mol Biol. 2006;360(3):573-85. DOI:10.1016/j.jmb.2006.04.047 |
7. Collén PN, Jeudy A, Sassi JF, Groisillier A, Czjzek M, Coutinho PM, and Helbert W. (2014). A novel unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105. J Biol Chem. 2014;289(9):6199-211. DOI:10.1074/jbc.M113.537480 |

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

9. Jongkees SAK, Yoo H, and Withers SG. (2014). Mechanistic investigations of unsaturated glucuronyl hydrolase from Clostridium perfringens. J Biol Chem. 2014;289(16):11385-11395. DOI:10.1074/jbc.M113.545293 |
10. 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 |
11. Jongkees SA and Withers SG. (2011). Glycoside cleavage by a new mechanism in unsaturated glucuronyl hydrolases. J Am Chem Soc. 2011;133(48):19334-7. DOI:10.1021/ja209067v |
12. Rye CS and Withers SG. (2000). Glycosidase mechanisms. Curr Opin Chem Biol. 2000;4(5):573-80. DOI:10.1016/s1367-5931(00)00135-6 |
13. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, and Ferrin TE. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605-12. DOI:10.1002/jcc.20084 |

14. 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].

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

16. Fellahi S, El Harrak M, Ducatez M, Loutfi C, Koraichi SI, Kuhn JH, Khayi S, El Houadfi M, and Ennaji MM. (2015). Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks. Virol J. 2015;12:116. DOI:10.1186/s12985-015-0347-8 |

17. 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].

18. 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].

19. 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].