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Difference between revisions of "Glycoside Hydrolase Family 78"
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== Substrate specificities == | == Substrate specificities == | ||
| − | Family GH78 glycoside hydrolases | + | Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, or polysaccharides such as rhamnogalacturonan and arabinogalactan-protein. |
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite> | + | GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR <cite>Zverlov2000</cite>. |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | The crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) indicated that Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule, and Glu895 appeared to be the catalytic general base <cite>Fujimoto2013</cite>. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | The first crystal structure was determined for ''Bacillus'' sp. GL1 α-L-rhamnosidase B (BsRhaB) <cite>Cui2007</cite>. | |
| + | Then, crystal structure of the putative α-L-rhamnosidase BT1001 from ''Bacteroides thetaiotaomicron'' VPI-5482 was determined by Structural genom project <cite>Bonanno2005</cite>. | ||
| + | Recently, crystal structure of ''Streptomyces avermitilis'' α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported <cite>Fujimoto2013</cite>. | ||
== Family Firsts == | == Family Firsts == | ||
| Line 53: | Line 55: | ||
#Cui2007 pmid=17936784 | #Cui2007 pmid=17936784 | ||
#Fujimoto2013 pmid=23486481 | #Fujimoto2013 pmid=23486481 | ||
| + | #Bonanno2005 pmid=16211523 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH078]] | [[Category:Glycoside Hydrolase Families|GH078]] | ||
Revision as of 21:41, 19 May 2014
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author:
- Responsible Curator: ^^^Zui Fujimoto^^^
| Glycoside Hydrolase Family GH78 | |
| Clan | GH-M |
| Mechanism | inverting |
| Active site residues | known |
| CAZy DB link | |
| http://www.cazy.org/GH78.html | |
Substrate specificities
Family GH78 glycoside hydrolases are found in bacteria and fungi. The characterized activity of this family is α-L-rhamnosidase (EC 3.2.1.40). α-L-Rhamnosidases catalyze the hydrolysis of α-L-rhamnosyl-linkages in L-rhamnose containing compounds, flavonoid glycosides such as naringin, hesperidin and rutin, or polysaccharides such as rhamnogalacturonan and arabinogalactan-protein.
Kinetics and Mechanism
GH78 enzymes hydrolyze glycosidic bonds through an acid base-assisted single displacement or inverting mechanism elucidated by proton NMR [1].
Catalytic Residues
The crystallographic and mutagenesis studies of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) indicated that Glu636 appeared to comprise the catalytic proton donor (acid) of the enzyme, activating a water molecule, and Glu895 appeared to be the catalytic general base [2].
Three-dimensional structures
The first crystal structure was determined for Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) [3]. Then, crystal structure of the putative α-L-rhamnosidase BT1001 from Bacteroides thetaiotaomicron VPI-5482 was determined by Structural genom project [4]. Recently, crystal structure of Streptomyces avermitilis α-L-rhamnosidase (SaRha78A) in complex with L-rhamnose was reported [2].
Family Firsts
- First stereochemistry determination
- Clostridium stercorarium α-L-rhamnosidase RamA, by 1H-NMR [1].
- First general base residue identification
- Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [2].
- First general acid residue identification
- Streptomyces avermitilis α-L-rhamnosidase (SaRha78A), based on mutagensis informed by 3D structural data [2].
- First 3-D structure
- Bacillus sp. GL1 α-L-rhamnosidase B (BsRhaB) [3].
References
- Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, and Schwarz WH. (2000). The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Mol Microbiol. 2000;35(1):173-9. DOI:10.1046/j.1365-2958.2000.01691.x |
- Fujimoto Z, Jackson A, Michikawa M, Maehara T, Momma M, Henrissat B, Gilbert HJ, and Kaneko S. (2013). The structure of a Streptomyces avermitilis α-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. J Biol Chem. 2013;288(17):12376-85. DOI:10.1074/jbc.M113.460097 |
- Cui Z, Maruyama Y, Mikami B, Hashimoto W, and Murata K. (2007). Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol. 2007;374(2):384-98. DOI:10.1016/j.jmb.2007.09.003 |
- Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, and Burley SK. (2005). New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005;6(2-3):225-32. DOI:10.1007/s10969-005-6827-0 |
- 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 |
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Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382