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Difference between revisions of "Glycoside Hydrolase Family 8"

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== Substrate specificities ==
 
== 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 [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-β-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 3.2.1.156]).
+
[[Glycoside hydrolases]] of family 8 cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (or xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-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 &beta;-D-xylose residues from the reducing end of xylooligosaccharides. The substrate specificities found in GH8 are: chitosanase (EC [{{EClink}}3.2.1.132 3.2.1.132]), cellulase (EC [{{EClink}}3.2.1.4 3.2.1.4]), licheninase (EC [{{EClink}}3.2.1.73 3.2.1.73]), endo-1,4-&beta;-xylanase (EC [{{EClink}}3.2.1.8 3.2.1.8]) and reducing-end-xylose releasing exo-oligoxylanase (EC [{{EClink}}3.2.1.156 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" <cite>Henrissat1989 Gilkes1991</cite>.
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
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#Fierobe1993 pmid=8223599
 
#Fierobe1993 pmid=8223599
 
#Beguin1985 pmid=3980433  
 
#Beguin1985 pmid=3980433  
#Petersen2009 pmid=19402614  
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#Petersen2009 pmid=19402614
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#Henrissat1989 pmid=2806912
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#Gilkes1991 pmid=1886523
 
</biblio>
 
</biblio>
  
 
[[Category:Glycoside Hydrolase Families|GH008]]
 
[[Category:Glycoside Hydrolase Families|GH008]]

Revision as of 09:14, 29 July 2015

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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. (1989). Cellulase families revealed by hydrophobic cluster analysis. Gene. 1989;81(1):83-95. DOI:10.1016/0378-1119(89)90339-9 | PubMed ID:2806912 [Henrissat1989]
  2. Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, and Warren RA. (1991). Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. Microbiol Rev. 1991;55(2):303-15. DOI:10.1128/mr.55.2.303-315.1991 | PubMed ID:1886523 [Gilkes1991]
  3. 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 [Fierobe1993]
  4. Petersen L, Ardèvol A, Rovira C, and Reilly PJ. (2009). Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. J Phys Chem B. 2009;113(20):7331-9. DOI:10.1021/jp811470d | PubMed ID:19402614 [Petersen2009]
  5. 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 [Alzari1996]
  6. 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 [Adachi2004]
  7. 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 [Guerin2002]
  8. 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 [Honda2006]
  9. 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 [Beguin1985]

All Medline abstracts: PubMed