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 See a page that's out-of-date and just needs a touch-up?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 8"

From CAZypedia
Jump to navigation Jump to search
Line 30: Line 30:
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The general acid (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <CITE>REF#4</CITE>.
+
The general acid (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite>REF#2</cite>.
The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <CITE>REF#4</CITE>.
+
The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <cite>REF#2</cite>.
 
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 <cite>REF1</cite>.
 
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 <cite>REF1</cite>.
  

Revision as of 18:45, 5 August 2009


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

Substrate specificities

GH8 enzymes 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 is 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).

Kinetics and Mechanism

GH8 enzymes are inverting enzymes, as first shown by Fiebrobe et al. on endoglucanase C from Clostridium cellulolyticum (CelCCC) [1].

Catalytic Residues

The general acid (proton donor to the leaving group) was first identified in CelA from C. thermocellum as Glu95 [2, 3]. The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from C. thermocellum as Asp278 [2, 3]. 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 [4].

Subfamilies

GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base [4]. 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 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 1kwf) has been determined [6].

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 [7].

Family Firsts

First gene cloning
Cellulase (celA) from Clostridium thermocellum [8]
First sterochemistry determination
Cite some reference here, with a short explanation .
First general acid residue identification
First general base residue identification of GH8a
First general base residue identification of GH8b
Chitosanase from Bacillus sp. K17 by crystal structure and a mutant [4].
First 3-D structure
Endoglucanase CelA from Clostridium thermocellum by X-ray crystallography (PDB 1cem) [5].

References

  1. Fierobe HP, Bagnara-Tardif C, Gaudin C, Guerlesquin F, Sauve P, Belaich A, and Belaich JP. (1993). Purification and characterization of endoglucanase C from Clostridium cellulolyticum. Catalytic comparison with endoglucanase A. Eur J Biochem. 1993;217(2):557-65. DOI:10.1111/j.1432-1033.1993.tb18277.x | PubMed ID:8223599 [REF5]
  2. Adachi W, Sakihama Y, Shimizu S, Sunami T, Fukazawa T, Suzuki M, Yatsunami R, Nakamura S, and Takénaka A. (2004). Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17. J Mol Biol. 2004;343(3):785-95. DOI:10.1016/j.jmb.2004.08.028 | PubMed ID:15465062 [REF1]
  3. Alzari PM, Souchon H, and Dominguez R. (1996). The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Structure. 1996;4(3):265-75. DOI:10.1016/s0969-2126(96)00031-7 | PubMed ID:8805535 [REF2]
  4. Guérin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Béguin P, and Alzari PM. (2002). Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002;316(5):1061-9. DOI:10.1006/jmbi.2001.5404 | PubMed ID:11884144 [REF3]
  5. Honda Y and Kitaoka M. (2006). The first glycosynthase derived from an inverting glycoside hydrolase. J Biol Chem. 2006;281(3):1426-31. DOI:10.1074/jbc.M511202200 | PubMed ID:16301312 [REF4]
  6. Béguin P, Cornet P, and Aubert JP. (1985). Sequence of a cellulase gene of the thermophilic bacterium Clostridium thermocellum. J Bacteriol. 1985;162(1):102-5. DOI:10.1128/jb.162.1.102-105.1985 | PubMed ID:3980433 [REF6]

All Medline abstracts: PubMed