CAZypedia needs your help! We have many unassigned GH, PL, CE, AA, GT, and CBM pages in need of Authors and Responsible Curators.
Scientists at all career stages, including students, are welcome to contribute to CAZypedia. Read more here, and in the 10th anniversary article in Glycobiology.
New to the CAZy classification? Read this first.
*
Consider attending the 15th Carbohydrate Bioengineering Meeting in Ghent, 5-8 May 2024.
Difference between revisions of "Glycoside Hydrolase Family 68"
Harry Brumer (talk | contribs) |
|||
(18 intermediate revisions by 5 users not shown) | |||
Line 1: | Line 1: | ||
<!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
{{CuratorApproved}} | {{CuratorApproved}} | ||
− | * [[Author]]: ^^^Tirso Pons^^^ and ^^^Wim Van den Ende^^^ | + | * [[Author]]: ^^^Tirso Pons^^^, ^^^Maxime Versluys^^^, and ^^^Wim Van den Ende^^^ |
* [[Responsible Curator]]: ^^^Wim Van den Ende^^^ | * [[Responsible Curator]]: ^^^Wim Van den Ende^^^ | ||
---- | ---- | ||
Line 22: | Line 22: | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
|- | |- | ||
− | | colspan="2" | | + | | colspan="2" |{{CAZyDBlink}}GH68.html |
|} | |} | ||
</div> | </div> | ||
Line 29: | Line 29: | ||
== Substrate specificities == | == Substrate specificities == | ||
− | Glycoside hydrolase family | + | [[Glycoside hydrolase]] family 68 enzymes include levansucrase (sucrose:2,6-β-D-fructan 6-β-D-fructosyltransferase; EC [{{EClink}}2.4.1.10 2.4.1.10]), β-fructofuranosidase (EC [{{EClink}}3.2.1.26 3.2.1.26]), and inulosucrase (EC [{{EClink}}2.4.1.9 2.4.1.9]). All these enzymes use sucrose as their preferential donor substrate. Many of them can create very long levan-type fructans (catalyzed by levansucrases) or inulin-type of fructans (catalyzed by inulosucrases), as well as fructooligosacharides (FOS). However, some GH68 enzymes can also use fructan as donor substrate (in the abscence of sucrose or at a high fructan/sucrose ratio). |
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
− | Family GH68 enzymes as well as those included in [[GH32]] | + | Family GH68 enzymes as well as those included in [[GH32]] are [[retaining]] enzymes <cite>Koshland1954</cite>. The levansucrases from ''Bacillus subtilis'', ''Gluconacetobacter diazotrophicus'', and ''Streptococcus salivarius'' catalyze transfructosylation via a ping-pong mechanism involving the formation of a transient fructosyl-enzyme intermediate <cite>Chambert1974 Cambert1976 Hernandez1995 Song1999</cite>. At low sucrose concentrations levansucrase functions as a hydrolase with water as acceptor, whereas at higher substrate concentrations it adds fructosyl units to a variety of acceptors including glucose, fructan and sucrose <cite>Chambert1974</cite>. Bacterial levansucrases, whatever their origin, catalyze all these reactions but with different efficiency. |
== Catalytic Residues == | == Catalytic Residues == | ||
− | + | GH68 [[retaining]] enzymes catalyze hydrolysis in two steps involving a covalent glycosyl enzyme [[intermediate]]. The two invariant residues, responsible for the catalytic reaction in family GH68 enzymes, have first been identified experimentally in bacterial levansucrases as an aspartate located close to the N-terminus acting as the [[catalytic nucleophile]] and a glutamate acting as the [[general acid/base]] <cite>Meng2003 Yanase2002</cite>. In addition, a conserved aspartate residue in the "Arg-Asp-Pro (RDP) motif" stabilizes the [[transition state]] <cite>Song1999 Yanase2002 Batista1999</cite>. The three equivalent acidic residues have been mutated in a β-fructofuranosidase from ''Arthrobacter globiformis'' IFO 3062 <cite>Isono2004</cite>, and in a levansucrase and a inulosucrase from ''Lactobacillus reuteri'' 121 <cite>Ozimek2004</cite>. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
− | Currently, | + | Currently, six different three dimensional structures of family GH68 enzymes have been solved. The first crystal structure was reported for the bacterial levansucrase (SacB) from ''Bacillus subtilis'' subsp. subtilis str. 168 <cite>Meng2003</cite>. The second one corresponds to levansucrase (LdsA) from ''Gluconacetobacter diazotrophicus'' SRT4 <cite>MartinezFleites2005</cite>, the third corresponds to SacB from ''Bacillus megaterium'' <cite>Strube2011</cite>, the fourth is an inulosucrase (InuJ) from ''Lactobacillus johnsonii'' NCC533 <cite>Pijning2011</cite> and the fifth one corresponds to beta-fructofuranosidase (ArFFase) from Arthrobacter sp. K-1 <cite>Tonozuca2012</cite>. More recently, the three dimensional structure of a levansucrase from ''Erwinia amylovora'' has been characterized as well <cite>Wuerges2015</cite>. These structures display a 5-fold β-propeller topology, and therefore GH families 68 and [[GH32|32]] have been combined in clan GH-J. On the other hand, a structural relationship of the catalytic core exists to family GH68 and family [[GH43]], as predicted by detailed sequence analysis <cite>Naumoff2001</cite>. |
== Family Firsts == | == Family Firsts == | ||
− | ;First stereochemistry determination: ''Bacillus subtilis'' levansucrase <cite> | + | ;First stereochemistry determination: ''Bacillus subtilis'' levansucrase <cite>Chambert1974</cite>. |
− | ;First catalytic nucleophile identification: ''Bacillus subtilis'' levansucrase <cite> | + | ;First [[catalytic nucleophile]] identification: ''Bacillus subtilis'' levansucrase <cite>Meng2003</cite>. |
− | ;First general acid/base residue identification: ''Zymomonas mobilis'' levansucrase <cite> | + | ;First [[general acid/base]] residue identification: ''Zymomonas mobilis'' levansucrase <cite>Yanase2002</cite>. |
− | ;First stabilizing transition | + | ;First stabilizing [[transition state]] residue identification: ''Gluconacetobacter diazotrophicus'' levansucrase <cite>Batista1999</cite>. |
− | ;First prediction of a common beta-propeller catalytic domain in GH68 / clan GH-J: ''Gluconacetobacter diazotrophicus'' levansucrase <cite> | + | ;First prediction of a common beta-propeller catalytic domain in GH68 / clan GH-J: ''Gluconacetobacter diazotrophicus'' levansucrase <cite>Pons1998 Pons2000</cite>. |
− | ;First 3-D structure: ''Bacillus subtilis'' levansucrase <cite> | + | ;First 3-D structure: ''Bacillus subtilis'' levansucrase <cite>Meng2003</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
− | # | + | #Koshland1954 pmid=13174523 |
− | # | + | #Chambert1974 pmid=4206083 |
− | # | + | #Chambert1976 pmid=814002 |
− | # | + | #Hernandez1995 pmid=7619044 |
− | # | + | #Song1999 pmid=10393084 |
− | # | + | #Meng2003 pmid=14517548 |
− | # | + | #Yanase2002 pmid=12359071 |
− | # | + | #Batista1999 pmid=9895294 |
− | # | + | #Isono2004 pmid=16233623 |
− | # | + | #Ozimek2004 pmid=14988011 |
− | # | + | #MartinezFleites2005 pmid=15869470 |
− | # | + | #Naumoff2001 pmid=11093261 |
− | # | + | #Pons1998 pmid=9829697 |
− | # | + | #Pons2000 pmid=11305239 |
+ | #Strube2011 pmid=21454585 | ||
+ | #Pijning2011 pmid=21801732 | ||
+ | #Tonozuca2012 pmid=23040392 | ||
+ | #Wuerges2015 pmid=26208466 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH068]] | [[Category:Glycoside Hydrolase Families|GH068]] |
Revision as of 09:09, 3 February 2017
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
- Author: ^^^Tirso Pons^^^, ^^^Maxime Versluys^^^, and ^^^Wim Van den Ende^^^
- Responsible Curator: ^^^Wim Van den Ende^^^
Glycoside Hydrolase Family GH68 | |
Clan | GH-J |
Mechanism | retaining |
Active site residues | known |
CAZy DB link | |
http://www.cazy.org/GH68.html |
Substrate specificities
Glycoside hydrolase family 68 enzymes include levansucrase (sucrose:2,6-β-D-fructan 6-β-D-fructosyltransferase; EC 2.4.1.10), β-fructofuranosidase (EC 3.2.1.26), and inulosucrase (EC 2.4.1.9). All these enzymes use sucrose as their preferential donor substrate. Many of them can create very long levan-type fructans (catalyzed by levansucrases) or inulin-type of fructans (catalyzed by inulosucrases), as well as fructooligosacharides (FOS). However, some GH68 enzymes can also use fructan as donor substrate (in the abscence of sucrose or at a high fructan/sucrose ratio).
Kinetics and Mechanism
Family GH68 enzymes as well as those included in GH32 are retaining enzymes [1]. The levansucrases from Bacillus subtilis, Gluconacetobacter diazotrophicus, and Streptococcus salivarius catalyze transfructosylation via a ping-pong mechanism involving the formation of a transient fructosyl-enzyme intermediate [2, 3, 4, 5]. At low sucrose concentrations levansucrase functions as a hydrolase with water as acceptor, whereas at higher substrate concentrations it adds fructosyl units to a variety of acceptors including glucose, fructan and sucrose [2]. Bacterial levansucrases, whatever their origin, catalyze all these reactions but with different efficiency.
Catalytic Residues
GH68 retaining enzymes catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate. The two invariant residues, responsible for the catalytic reaction in family GH68 enzymes, have first been identified experimentally in bacterial levansucrases as an aspartate located close to the N-terminus acting as the catalytic nucleophile and a glutamate acting as the general acid/base [6, 7]. In addition, a conserved aspartate residue in the "Arg-Asp-Pro (RDP) motif" stabilizes the transition state [5, 7, 8]. The three equivalent acidic residues have been mutated in a β-fructofuranosidase from Arthrobacter globiformis IFO 3062 [9], and in a levansucrase and a inulosucrase from Lactobacillus reuteri 121 [10].
Three-dimensional structures
Currently, six different three dimensional structures of family GH68 enzymes have been solved. The first crystal structure was reported for the bacterial levansucrase (SacB) from Bacillus subtilis subsp. subtilis str. 168 [6]. The second one corresponds to levansucrase (LdsA) from Gluconacetobacter diazotrophicus SRT4 [11], the third corresponds to SacB from Bacillus megaterium [12], the fourth is an inulosucrase (InuJ) from Lactobacillus johnsonii NCC533 [13] and the fifth one corresponds to beta-fructofuranosidase (ArFFase) from Arthrobacter sp. K-1 [14]. More recently, the three dimensional structure of a levansucrase from Erwinia amylovora has been characterized as well [15]. These structures display a 5-fold β-propeller topology, and therefore GH families 68 and 32 have been combined in clan GH-J. On the other hand, a structural relationship of the catalytic core exists to family GH68 and family GH43, as predicted by detailed sequence analysis [16].
Family Firsts
- First stereochemistry determination
- Bacillus subtilis levansucrase [2].
- First catalytic nucleophile identification
- Bacillus subtilis levansucrase [6].
- First general acid/base residue identification
- Zymomonas mobilis levansucrase [7].
- First stabilizing transition state residue identification
- Gluconacetobacter diazotrophicus levansucrase [8].
- First prediction of a common beta-propeller catalytic domain in GH68 / clan GH-J
- Gluconacetobacter diazotrophicus levansucrase [17, 18].
- First 3-D structure
- Bacillus subtilis levansucrase [6].
References
- KOSHLAND DE Jr and STEIN SS. (1954). Correlation of bond breaking with enzyme specificity; cleavage point of invertase. J Biol Chem. 1954;208(1):139-48. | Google Books | Open Library
- Chambert R, Treboul G, and Dedonder R. (1974). Kinetic studies of levansucrase of Bacillus subtilis. Eur J Biochem. 1974;41(2):285-300. DOI:10.1111/j.1432-1033.1974.tb03269.x |
- Hernandez L, Arrieta J, Menendez C, Vazquez R, Coego A, Suarez V, Selman G, Petit-Glatron MF, and Chambert R. (1995). Isolation and enzymic properties of levansucrase secreted by Acetobacter diazotrophicus SRT4, a bacterium associated with sugar cane. Biochem J. 1995;309 ( Pt 1)(Pt 1):113-8. DOI:10.1042/bj3090113 |
- Song DD and Jacques NA. (1999). Purification and enzymic properties of the fructosyltransferase of Streptococcus salivarius ATCC 25975. Biochem J. 1999;341 ( Pt 2)(Pt 2):285-91. | Google Books | Open Library
- Meng G and Fütterer K. (2003). Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Biol. 2003;10(11):935-41. DOI:10.1038/nsb974 |
- Yanase H, Maeda M, Hagiwara E, Yagi H, Taniguchi K, and Okamoto K. (2002). Identification of functionally important amino acid residues in Zymomonas mobilis levansucrase. J Biochem. 2002;132(4):565-72. DOI:10.1093/oxfordjournals.jbchem.a003258 |
- Batista FR, Hernández L, Fernández JR, Arrieta J, Menéndez C, Gómez R, Támbara Y, and Pons T. (1999). Substitution of Asp-309 by Asn in the Arg-Asp-Pro (RDP) motif of Acetobacter diazotrophicus levansucrase affects sucrose hydrolysis, but not enzyme specificity. Biochem J. 1999;337 ( Pt 3)(Pt 3):503-6. | Google Books | Open Library
- Isono N, Tochihara T, Kusnadi Y, Win TT, Watanabe K, Obae K, Ito H, and Matsui H. (2004). Cloning and heterologous expression of a beta-fructofuranosidase gene from Arthrobacter globiformis IFO 3062, and site-directed mutagenesis of the essential aspartic acid and glutamic acid of the active site. J Biosci Bioeng. 2004;97(4):244-9. DOI:10.1016/S1389-1723(04)70199-1 |
- Ozimek LK, van Hijum SA, van Koningsveld GA, van Der Maarel MJ, van Geel-Schutten GH, and Dijkhuizen L. (2004). Site-directed mutagenesis study of the three catalytic residues of the fructosyltransferases of Lactobacillus reuteri 121. FEBS Lett. 2004;560(1-3):131-3. DOI:10.1016/S0014-5793(04)00085-7 |
- Martínez-Fleites C, Ortíz-Lombardía M, Pons T, Tarbouriech N, Taylor EJ, Arrieta JG, Hernández L, and Davies GJ. (2005). Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus. Biochem J. 2005;390(Pt 1):19-27. DOI:10.1042/BJ20050324 |
- Strube CP, Homann A, Gamer M, Jahn D, Seibel J, and Heinz DW. (2011). Polysaccharide synthesis of the levansucrase SacB from Bacillus megaterium is controlled by distinct surface motifs. J Biol Chem. 2011;286(20):17593-600. DOI:10.1074/jbc.M110.203166 |
- Pijning T, Anwar MA, Böger M, Dobruchowska JM, Leemhuis H, Kralj S, Dijkhuizen L, and Dijkstra BW. (2011). Crystal structure of inulosucrase from Lactobacillus: insights into the substrate specificity and product specificity of GH68 fructansucrases. J Mol Biol. 2011;412(1):80-93. DOI:10.1016/j.jmb.2011.07.031 |
- Tonozuka T, Tamaki A, Yokoi G, Miyazaki T, Ichikawa M, Nishikawa A, Ohta Y, Hidaka Y, Katayama K, Hatada Y, Ito T, and Fujita K. (2012). Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 β-fructofuranosidase. Enzyme Microb Technol. 2012;51(6-7):359-65. DOI:10.1016/j.enzmictec.2012.08.004 |
- Wuerges J, Caputi L, Cianci M, Boivin S, Meijers R, and Benini S. (2015). The crystal structure of Erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site. J Struct Biol. 2015;191(3):290-8. DOI:10.1016/j.jsb.2015.07.010 |
- Naumoff DG (2001). beta-fructosidase superfamily: homology with some alpha-L-arabinases and beta-D-xylosidases. Proteins. 2001;42(1):66-76. DOI:10.1002/1097-0134(20010101)42:1<66::aid-prot70>3.0.co;2-4 |
- Pons T, Olmea O, Chinea G, Beldarraín A, Márquez G, Acosta N, Rodríguez L, and Valencia A. (1998). Structural model for family 32 of glycosyl-hydrolase enzymes. Proteins. 1998;33(3):383-95. DOI:10.1002/(sici)1097-0134(19981115)33:3<383::aid-prot7>3.0.co;2-r |
- Pons T, Hernández L, Batista FR, and Chinea G. (2000). Prediction of a common beta-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity. Protein Sci. 2000;9(11):2285-91. DOI:10.1110/ps.9.11.2285 |
- Chambert R and Gonzy-Tréboul G. (1976). Levansucrase of Bacillus subtilis: kinetic and thermodynamic aspects of transfructosylation processes. Eur J Biochem. 1976;62(1):55-64. DOI:10.1111/j.1432-1033.1976.tb10097.x |