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Difference between revisions of "Glycoside Hydrolase Family 8"

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* [[Author]]: [[User:MotomitsuKitaoka|Motomitsu Kitaoka]]
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* [[Responsible Curator]]:  [[User:ShinyaFushinobu|Shinya Fushinobu]]
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* [[Author]]s: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]] and [[User:Shinya Fushinobu|Shinya Fushinobu]]
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* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|-
 
|-
| colspan="2" |http://www.cazy.org/fam/GH8.html
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| colspan="2" |{{CAZyDBlink}}GH8.html
 
|}
 
|}
 
</div>
 
</div>
  
 
== Substrate specificities ==
 
== Substrate specificities ==
GH8 enzymes cleave &beta;-1,4 linkages of &beta;-1,4 glucans, xylans (xylooligosaccharides), chitosans, and lichenans (1,3-1,4-&beta;-D-glucan). 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 3.2.1.132), cellulase (EC 3.2.1.4), licheninase (EC 3.2.1.73), endo-1,4-&beta;-xylanase (EC 3.2.1.8) and reducing-end-xylose releasing exo-oligoxylanase (EC 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 ==
GH8 enzymes are inverting enzymes, as first shown by ... (ref) on ... from ....
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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 <CITE>Fierobe1993</CITE>. Hydrolysis by CelA was computationally simulated with QM/MM metadynamics <CITE>Petersen2009</CITE>.
 
+
=== Glycosynthase engineering ===
 +
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 <cite>Honda2006</cite>.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The catalytic acid (proton donor) was first suggested/identified in ... as Glu...
+
The [[general acid]] (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite>Alzari1996</cite>.
The catalytic base (proton acceptor) of GH8a subfamily was first suggested/identified in ... as Asp...
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The [[general base]] (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <cite>Alzari1996</cite>.
The catalytic 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>Adachi2004</cite>.
 
 
== Subfamilies ==
 
GH8 enzymes are divided into at least three subfamilies, depending on the position of the catalytic base <cite>REF1</cite>.
 
GH8a has the catalytic base (Asp) at the N-terminal end of &alpha;8 helix. GH8a contains cellulases, xylanases and other enzymes.
 
In GH8b enzymes, the Asp residue is replaced by Asn, and the catalytic base is a Glu residue located in a long loop inserted between &alpha;7 and &alpha;8 helices. GH8b contains chitosanases, licheninases, cellulases and other enzymes.
 
The position of the catalytic base in GH8c is unknown.
 
  
 
== Three-dimensional structures ==
 
== 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'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1CEM PDB 1cem]) in 1996 <cite>REF2</cite>. As members of Clan GH-M they have a (&alpha;/&alpha;)<sub>6</sub> fold similar to [[Glycoside Hydrolase Family 48]]. The catalytic acid residue is located at the N-terminal end of &alpha;4 helix. Position of the catalytic base differ among [[#Subfamilies]]. Atomic (0.94 &Aring;) resolution structure of CelA in complex with substrate ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1KWF PDB 1kwf]) has been determined <cite>REF3</cite>.
+
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 [{{PDBlink}}1cem 1cem]) in 1996 <cite>Alzari1996</cite>. As members of Clan GH-M they have a (&alpha;/&alpha;)<sub>6</sub> fold similar to [[Glycoside Hydrolase Family 48]]. The general acid residue is located at the N-terminal end of &alpha;4 helix. Position of the general base differ among [[#Subfamilies]]. Atomic (0.94 &Aring;) resolution structure of CelA in complex with substrate (PDB ID [{{PDBlink}}1kwf 1kwf]) has been determined <cite>Guerin2002</cite>.
 +
=== Subfamilies ===
 +
GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base <cite>Adachi2004</cite>.
 +
GH8a has the general base (Asp) at the N-terminal end of &alpha;8 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 &alpha;7 and &alpha;8 helices. GH8b contains chitosanases, licheninases, cellulases and other enzymes.
 +
The position of the general base in GH8c is unknown.
  
 
== Family Firsts ==
 
== Family Firsts ==
;First sterochemistry determination: Cite some reference here, with a ''short'' explanation .
+
;First sequence identification: Cellulase (''celA'') from ''Clostridium thermocellum'' <cite>Beguin1985</cite>
;First catalytic acid residue identification:  
+
;First sterochemistry determination: Endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) <cite>Fierobe1993</cite>
;First catalytic base residue identification of GH8a:  
+
;First [[general acid]] residue identification: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite>
;First catalytic base residue identification of GH8b: Chitosanase from ''Bacillus'' sp. K17 by crystal structure and a mutant <cite>REF1</cite>.
+
;First [[general base]] residue identification of GH8a: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite>
;First 3-D structure: Endoglucanase CelA from ''Clostridium thermocellum'' by X-ray crystallography  ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1CEM PDB 1cem]) <cite>REF2</cite>.
+
;First [[general base]] residue identification of GH8b: Chitosanase from ''Bacillus'' sp. K17 by crystal structure and a mutant <cite>Adachi2004</cite>.
 
+
;First 3-D structure: Endoglucanase CelA from ''Clostridium thermocellum'' by X-ray crystallography  (PDB ID [{{PDBlink}}1cem 1cem]) <cite>Alzari1996</cite>.
== Glycosynthase ==
 
Reducing-end-xylose releasing exo-oligoxylanase from ''Bacillus halodurans'' C-125 is the first inverting enzyme that was converted to glycosynthase by mutating the catalytic base residue <cite>REF4</cite>.
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#REF1 pmid=15465062
+
#Adachi2004 pmid=15465062
#REF2 pmid=8805535
+
#Alzari1996 pmid=8805535
#REF3 pmid=11884144
+
#Guerin2002 pmid=11884144
#REF4 pmid=16301312
+
#Honda2006 pmid=16301312
 +
#Fierobe1993 pmid=8223599
 +
#Beguin1985 pmid=3980433
 +
#Petersen2009 pmid=19402614
 +
#Henrissat1989 pmid=2806912
 +
#Gilkes1991 pmid=1886523
 
</biblio>
 
</biblio>
  
[[Category:Glycoside Hydrolase Families]]
+
[[Category:Glycoside Hydrolase Families|GH008]]

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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 was computationally simulated with QM/MM metadynamics [4].

Glycosynthase engineering

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 [5].

Catalytic Residues

The general acid (proton donor to the leaving group) was first identified in CelA from C. thermocellum as Glu95 [6]. The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from C. thermocellum as Asp278 [6]. 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 [7].

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 [6]. 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 [8].

Subfamilies

GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base [7]. 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.

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 [6]
First general base residue identification of GH8a
Cellulase (CelA) from Clostridium thermocellum [6]
First general base residue identification of GH8b
Chitosanase from Bacillus sp. K17 by crystal structure and a mutant [7].
First 3-D structure
Endoglucanase CelA from Clostridium thermocellum by X-ray crystallography (PDB ID 1cem) [6].

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. 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]
  6. 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]
  7. 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]
  8. 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]
  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