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Glycoside Hydrolase Family 8

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Glycoside Hydrolase Family 8
Clan GH-M
Mechanism inverting
Active site residues known
CAZy DB link
http://www.cazy.org/GH8.html

Substrate specificities

Glycoside hydrolases of family 8 cleave β-1,4 linkages of β-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-β-D-glucan). All of GH8 members have been found from bacteria, and there are no members from Eukaryotic or Archaeal origin. The majority of the enzymes are endo-acting enzymes, but one member has an exo-activity that releases β-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC 3.2.1.132), cellulase (EC 3.2.1.4), licheninase (EC 3.2.1.73), endo-1,4-β-xylanase (EC 3.2.1.8) and reducing-end-xylose releasing exo-oligoxylanase (EC 3.2.1.156). GH8 was one of the first glycoside hydrolase families classified by hydrophobic cluster analysis, and was previously known as "Cellulase Family D" [1, 2].

Kinetics and Mechanism

Enzymes of glycoside hydrolase family 8 are inverting enzymes, as first shown by Fierobe et al. who monitored the reaction of endoglucanase C from Clostridium cellulolyticum (CelCCC) using proton NMR spectroscopy [3]. Hydrolysis by CelA is computationally simulated with QM/MM metadynamics [4].

Catalytic Residues

The general acid (proton donor to the leaving group) was first identified in CelA from C. thermocellum as Glu95 [5]. The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from C. thermocellum as Asp278 [5]. The general base of GH8b subfamily was first identified in chitosanase from Bacillus sp. K17 as Glu309 based on its crystal structure and by making E309Q mutant [6].

Subfamilies

GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base [6]. GH8a has the general base (Asp) at the N-terminal end of α8 helix. GH8a contains cellulases, xylanases and other enzymes. In GH8b enzymes, the Asp residue is replaced by Asn, and the general base is a Glu residue located in a long loop inserted between α7 and α8 helices. GH8b contains chitosanases, licheninases, cellulases and other enzymes. The position of the general base in GH8c is unknown.

Three-dimensional structures

Several three-dimensional structures of GH8 members from bacterial origin have been solved. The first solved 3-D structure was endoglucanase CelA from Clostridium thermocellum (PDB ID 1cem) in 1996 [5]. As members of Clan GH-M they have a (α/α)6 fold similar to Glycoside Hydrolase Family 48. The general acid residue is located at the N-terminal end of α4 helix. Position of the general base differ among #Subfamilies. Atomic (0.94 Å) resolution structure of CelA in complex with substrate (PDB ID 1kwf) has been determined [7].

Glycosynthase

Reducing-end-xylose releasing exo-oligoxylanase from Bacillus halodurans C-125 is the first inverting GH that was converted to glycosynthase by mutating the general base residue [8].

Family Firsts

First sequence identification
Cellulase (celA) from Clostridium thermocellum [9]
First sterochemistry determination
Endoglucanase C from Clostridium cellulolyticum (CelCCC) [3]
First general acid residue identification
Cellulase (CelA) from Clostridium thermocellum [5]
First general base residue identification of GH8a
Cellulase (CelA) from Clostridium thermocellum [5]
First general base residue identification of GH8b
Chitosanase from Bacillus sp. K17 by crystal structure and a mutant [6].
First 3-D structure
Endoglucanase CelA from Clostridium thermocellum by X-ray crystallography (PDB ID 1cem) [5].

References

  1. Henrissat B, Claeyssens M, Tomme P, Lemesle L, and Mornon JP. Cellulase families revealed by hydrophobic cluster analysis. Gene. 1989 Sep 1;81(1):83-95. PubMed ID:2806912 | HubMed [Henrissat1989]
  2. Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, and Warren RA. Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. Microbiol Rev. 1991 Jun;55(2):303-15. PubMed ID:1886523 | HubMed [Gilkes1991]
  3. Fierobe HP, Bagnara-Tardif C, Gaudin C, Guerlesquin F, Sauve P, Belaich A, and Belaich JP. Purification and characterization of endoglucanase C from Clostridium cellulolyticum. Catalytic comparison with endoglucanase A. Eur J Biochem. 1993 Oct 15;217(2):557-65. PubMed ID:8223599 | HubMed [Fierobe1993]
  4. Petersen L, Ardèvol A, Rovira C, and Reilly PJ. Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. J Phys Chem B. 2009 May 21;113(20):7331-9. DOI:10.1021/jp811470d | PubMed ID:19402614 | HubMed [Petersen2009]
  5. Alzari PM, Souchon H, and Dominguez R. The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Structure. 1996 Mar 15;4(3):265-75. PubMed ID:8805535 | HubMed [Alzari1996]
  6. Adachi W, Sakihama Y, Shimizu S, Sunami T, Fukazawa T, Suzuki M, Yatsunami R, Nakamura S, and Takénaka A. Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17. J Mol Biol. 2004 Oct 22;343(3):785-95. DOI:10.1016/j.jmb.2004.08.028 | PubMed ID:15465062 | HubMed [Adachi2004]
  7. Guérin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Béguin P, and Alzari PM. Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002 Mar 8;316(5):1061-9. DOI:10.1006/jmbi.2001.5404 | PubMed ID:11884144 | HubMed [Guerin2002]
  8. Honda Y and Kitaoka M. The first glycosynthase derived from an inverting glycoside hydrolase. J Biol Chem. 2006 Jan 20;281(3):1426-31. DOI:10.1074/jbc.M511202200 | PubMed ID:16301312 | HubMed [Honda2006]
  9. Béguin P, Cornet P, and Aubert JP. Sequence of a cellulase gene of the thermophilic bacterium Clostridium thermocellum. J Bacteriol. 1985 Apr;162(1):102-5. PubMed ID:3980433 | HubMed [Beguin1985]
All Medline abstracts: PubMed | HubMed
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