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Glycoside Hydrolase Family 105

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Glycoside Hydrolase Family GH105
Clan GH-x
Mechanism retaining/inverting
Active site residues known/not known
CAZy DB link
http://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

  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. 37, D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
  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. 292, 13271-13283. DOI:10.1074/jbc.M117.794578 | PubMed ID:28637865 | HubMed [Munoz-Munoz2017]
  3. Jongkees SA and Withers SG. (2011) Glycoside cleavage by a new mechanism in unsaturated glucuronyl hydrolases. J Am Chem Soc. 133, 19334-7. DOI:10.1021/ja209067v | PubMed ID:22047074 | HubMed [Jongkees2011]
  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. 60, 561-5. DOI:10.1002/prot.20410 | PubMed ID:15906318 | HubMed [Zhang2009]
  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. 347, 1021-9. DOI:10.1016/j.bbrc.2006.07.034 | PubMed ID:16870154 | HubMed [Itoh2006]
  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. 360, 573-85. DOI:10.1016/j.jmb.2006.04.047 | PubMed ID:16781735 | HubMed [Itoh2006-1]
  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. 289, 6199-211. DOI:10.1074/jbc.M113.537480 | PubMed ID:24407291 | HubMed [Collen2014]
  8. Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. Biological Reviews, vol. 28, no. 4., pp. 416-436. [1].
    [Koshland1953]
  9. Jongkees SA, Yoo H, and Withers SG. (2014) Mechanistic investigations of unsaturated glucuronyl hydrolase from Clostridium perfringens. J Biol Chem. 289, 11385-95. DOI:10.1074/jbc.M113.545293 | PubMed ID:24573682 | HubMed [Jongkees2014]
  10. Rye CS and Withers SG. (2000) Glycosidase mechanisms. Curr Opin Chem Biol. 4, 573-80. PubMed ID:11006547 | HubMed [Rye2000]
  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. 25, 1605-12. DOI:10.1002/jcc.20084 | PubMed ID:15264254 | HubMed [Pettersen2004]
  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].
    [JCSG2009]
  13. Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. RCSB Protein Data Bank. [1].
    [Osipiuk2014]
  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. 71, 1100-8. DOI:10.1107/S2053230X15012121 | PubMed ID:26249707 | HubMed [Germane2015]
  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].
    [Tan2010]
  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].
    [Tan2011]
  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].
    [Stogios2015]
All Medline abstracts: PubMed | HubMed