CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.

Difference between revisions of "Glycoside Hydrolase Family 16"

From CAZypedia
Jump to navigation Jump to search
Line 36: Line 36:
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
Several family 16 three-dimensional structures have been solved of both archeal, bacterial and eukaryotic origin. The first solved 3-D structure was a hybrid protein of lichenase M from ''Paenibacillus macerans'' and BglA from ''Bacillus amyloliquefaciens'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1BYH PDB 1byh]) in 1992 <cite>5</cite>.  
+
Several family 16 three-dimensional structures have been solved of archeal, bacterial and eukaryotic origin. The first solved 3-D structure was a hybrid protein of lichenase M from ''Paenibacillus macerans'' and BglA from ''Bacillus amyloliquefaciens'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1BYH PDB 1byh]) in 1992 <cite>5</cite>.  
 
The first eukaryotic 3-D structure was the xyloglucan ''endo''-transglycosylase ''Ptt''XET16-34 from ''Populus tremula&times;tremuloides'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1UMZ PDB 1umz]) <cite>REF1</cite>. The first archeal 3-D structure was a ''endo''-1,3-&beta;-glucanase Lam16 from ''Pyrococcus furiosus'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=2VY0 PDB 2vy0]) <cite>8</cite>.
 
The first eukaryotic 3-D structure was the xyloglucan ''endo''-transglycosylase ''Ptt''XET16-34 from ''Populus tremula&times;tremuloides'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1UMZ PDB 1umz]) <cite>REF1</cite>. The first archeal 3-D structure was a ''endo''-1,3-&beta;-glucanase Lam16 from ''Pyrococcus furiosus'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=2VY0 PDB 2vy0]) <cite>8</cite>.
  

Revision as of 10:11, 1 June 2009


Glycoside Hydrolase Family 16
Clan GH-B
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/fam/GH16.html

Substrate specificities

Family 16 enzymes cleave β-1,4 or β-1,3 glycosidic bonds in various glucans and galactans. Some members of this family operating on xyloglucan exhibit predominant endo-transglycosylase activity [1]. The substrate specificities found in GH16 are: xyloglucan:xyloglucosyltransferases (EC 2.4.1.207), keratan-sulfate endo-1,4-β-galactosidases (EC 3.2.1.103), endo-1,3-β-glucanases (EC 3.2.1.39), endo-1,3(4)-β-glucanases (EC 3.2.1.6), lichenases (EC 3.2.1.73), β-agarases (EC 3.2.1.81), κ-carrageenases (EC 3.2.1.83) and xyloglucanases (EC 3.2.1.151).

Kinetics and Mechanism

Family 16 enzymes are retaining enzymes, as first shown by NMR [2] on an endo-1,3-1,4-β-D-glucan 4-glucanohydrolase from Bacillus licheniformis.

Catalytic Residues

The nucleophile was first suggested using an epoxyalkyl β-glycoside inhibitor and subsequent peptide identification by ESI-MS and Edman degradation on an endo-1,3-1,4-β-D-glucan 4-glucanohydrolase from Bacillus amyloliquefaciens [3]. This was subsequently verified by azide rescue of the E134A mutant of a Bacillus licheniformis 1,3-1,4-β-D-glucan 4-glucanohydrolase resulting in an α-glycosyl product from the β-glycosyl substrate [4]. The acid-base was found by making the E138A mutant from the Bacillus licheniformis 1,3-1,4-β-D-glucan 4-glucanohydrolase and subsequent azide rescue resulting in a β-glycosyl azide product [4].

Three-dimensional structures

Several family 16 three-dimensional structures have been solved of archeal, bacterial and eukaryotic origin. The first solved 3-D structure was a hybrid protein of lichenase M from Paenibacillus macerans and BglA from Bacillus amyloliquefaciens (PDB 1byh) in 1992 [5]. The first eukaryotic 3-D structure was the xyloglucan endo-transglycosylase PttXET16-34 from Populus tremula×tremuloides (PDB 1umz) [6]. The first archeal 3-D structure was a endo-1,3-β-glucanase Lam16 from Pyrococcus furiosus (PDB 2vy0) [7].

Evolution of GH16

Family 16 is a member of clan GH-B together with family 7 with whom they share their β-jellyroll fold. The different specificities of family 16 has been proposed to have evoloved from an ancestral β-1,3-glucanase [8]. The first branching in family 16 lead to the evolution of the κ-carrageenases and the β-agarases and a later branching event lead to the arisal of the lichenases and the XETs [9] (see figure).

Evolution of family 16

Family firsts

First stereochemistry determination
Bacillus licheniformis 1,3-1,4-β-D-glucan 4-glucanohydrolase by NMR [2].
First nucleophile identification
Suggested in Bacillus amyloliquefaciens 1,3-1,4-β-D-glucan 4-glucanohydrolase [3]. Later verified in by azide rescue of inactivated mutants [4].
First general acid/base residue identification
Bacillus licheniformis 1,3-1,4-β-D-glucan 4-glucanohydrolase, first suggested by sequence homology and mutational studies [10]. This was later verified by azide rescue of inactivated mutants [4].
First 3-D structure
A hybrid lichenase (Bacillus amyloliquefaciens and Paenibacillus macerans) by X-ray crystallography (PDB 1byh) [5].

Reference list

  1. Baumann MJ, Eklöf JM, Michel G, Kallas AM, Teeri TT, Czjzek M, and Brumer H 3rd. (2007). Structural evidence for the evolution of xyloglucanase activity from xyloglucan endo-transglycosylases: biological implications for cell wall metabolism. Plant Cell. 2007;19(6):1947-63. DOI:10.1105/tpc.107.051391 | PubMed ID:17557806 [NXG]
  2. Malet C, Jiménez-Barbero J, Bernabé M, Brosa C, and Planas A. (1993). Stereochemical course and structure of the products of the enzymic action of endo-1,3-1,4-beta-D-glucan 4-glucanohydrolase from Bacillus licheniformis. Biochem J. 1993;296 ( Pt 3)(Pt 3):753-8. DOI:10.1042/bj2960753 | PubMed ID:8280073 [REF3]
  3. Høj PB, Condron R, Traeger JC, McAuliffe JC, and Stone BA. (1992). Identification of glutamic acid 105 at the active site of Bacillus amyloliquefaciens 1,3-1,4-beta-D-glucan 4-glucanohydrolase using epoxide-based inhibitors. J Biol Chem. 1992;267(35):25059-66. | Google Books | Open Library PubMed ID:1360982 [REF4]
  4. Viladot JL, de Ramon E, Durany O, and Planas A. (1998). Probing the mechanism of Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases by chemical rescue of inactive mutants at catalytically essential residues. Biochemistry. 1998;37(32):11332-42. DOI:10.1021/bi980586q | PubMed ID:9698381 [7]
  5. Keitel T, Simon O, Borriss R, and Heinemann U. (1993). Molecular and active-site structure of a Bacillus 1,3-1,4-beta-glucanase. Proc Natl Acad Sci U S A. 1993;90(11):5287-91. DOI:10.1073/pnas.90.11.5287 | PubMed ID:8099449 [5]
  6. Johansson P, Brumer H 3rd, Baumann MJ, Kallas AM, Henriksson H, Denman SE, Teeri TT, and Jones TA. (2004). Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding. Plant Cell. 2004;16(4):874-86. DOI:10.1105/tpc.020065 | PubMed ID:15020748 [REF1]
  7. Ilari A, Fiorillo A, Angelaccio S, Florio R, Chiaraluce R, van der Oost J, and Consalvi V. (2009). Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus--structural basis of substrate recognition. FEBS J. 2009;276(4):1048-58. DOI:10.1111/j.1742-4658.2008.06848.x | PubMed ID:19154353 [8]
  8. Barbeyron T, Gerard A, Potin P, Henrissat B, and Kloareg B. (1998). The kappa-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases. Mol Biol Evol. 1998;15(5):528-37. DOI:10.1093/oxfordjournals.molbev.a025952 | PubMed ID:9580981 [10]
  9. Michel G, Chantalat L, Duee E, Barbeyron T, Henrissat B, Kloareg B, and Dideberg O. (2001). The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases. Structure. 2001;9(6):513-25. DOI:10.1016/s0969-2126(01)00612-8 | PubMed ID:11435116 [9]
  10. Juncosa M, Pons J, Dot T, Querol E, and Planas A. (1994). Identification of active site carboxylic residues in Bacillus licheniformis 1,3-1,4-beta-D-glucan 4-glucanohydrolase by site-directed mutagenesis. J Biol Chem. 1994;269(20):14530-5. | Google Books | Open Library PubMed ID:8182059 [6]

All Medline abstracts: PubMed