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Difference between revisions of "Glycoside Hydrolase Family 8"
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− | * [[Author]]: [[User: | + | {{CuratorApproved}} |
− | * [[Responsible Curator]]: [[User: | + | * [[Author]]s: [[User:Motomitsu Kitaoka|Motomitsu Kitaoka]] and [[User:Shinya Fushinobu|Shinya Fushinobu]] |
+ | * [[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" | | + | | colspan="2" |{{CAZyDBlink}}GH8.html |
|} | |} | ||
</div> | </div> | ||
== 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]). 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 == | ||
− | + | 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 general acid (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite> | + | The [[general acid]] (proton donor to the leaving group) was first identified in CelA from ''C. thermocellum'' as Glu95 <cite>Alzari1996</cite>. |
− | The general base (proton acceptor from the nucleophilic water) of GH8a subfamily was first identified in CelA from ''C. thermocellum'' as Asp278 <cite> | + | 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 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> | + | 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 == | + | == Three-dimensional structures == |
− | GH8 enzymes are divided into at least three subfamilies, depending on the position of the general base <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 (α/α)<sub>6</sub> 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 [{{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 α8 helix. GH8a contains cellulases, xylanases and other enzymes. | 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. | 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. | The position of the general base in GH8c is unknown. | ||
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== Family Firsts == | == Family Firsts == | ||
− | ;First | + | ;First sequence identification: Cellulase (''celA'') from ''Clostridium thermocellum'' <cite>Beguin1985</cite> |
− | ;First sterochemistry determination: | + | ;First sterochemistry determination: Endoglucanase C from ''Clostridium cellulolyticum'' (CelCCC) <cite>Fierobe1993</cite> |
− | ;First general acid residue identification: | + | ;First [[general acid]] residue identification: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite> |
− | ;First general base residue identification of GH8a: | + | ;First [[general base]] residue identification of GH8a: Cellulase (CelA) from ''Clostridium thermocellum'' <cite>Alzari1996</cite> |
− | ;First general base residue identification of GH8b: Chitosanase from ''Bacillus'' sp. K17 by crystal structure and a mutant <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 ([ | + | ;First 3-D structure: Endoglucanase CelA from ''Clostridium thermocellum'' by X-ray crystallography (PDB ID [{{PDBlink}}1cem 1cem]) <cite>Alzari1996</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
− | # | + | #Adachi2004 pmid=15465062 |
− | # | + | #Alzari1996 pmid=8805535 |
− | # | + | #Guerin2002 pmid=11884144 |
− | # | + | #Honda2006 pmid=16301312 |
− | # | + | #Fierobe1993 pmid=8223599 |
− | # | + | #Beguin1985 pmid=3980433 |
+ | #Petersen2009 pmid=19402614 | ||
+ | #Henrissat1989 pmid=2806912 | ||
+ | #Gilkes1991 pmid=1886523 | ||
</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families|GH008]] | [[Category:Glycoside Hydrolase Families|GH008]] |
Latest revision as of 14:15, 18 December 2021
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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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |