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].

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate [6]. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc [2].

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) [10].

Catalytic Residues

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis [5, 6]. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase [4]. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity [6]. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite [6]. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) [2, 7, 11].

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

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 |
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 |
3. 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 |
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. 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 |
11. 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 |

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].

14. Germane KL, Servinsky MD, Gerlach ES, Sund CJ, and Hurley MM. (2015). Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105. Acta Crystallogr F Struct Biol Commun. 2015;71(Pt 8):1100-8. DOI:10.1107/S2053230X15012121 |

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].