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Difference between revisions of "Glycoside Hydrolase Family 43"

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* [[Author]]: [[User:Harry Gilbert|Harry Gilbert]]
 
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|'''Active site residues'''
 
|'''Active site residues'''
|not known
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|Known
 
|-
 
|-
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|-
 
|-
| colspan="2" |http://www.cazy.org/fam/GH43.html
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| colspan="2" |{{CAZyDBlink}}GH43.html
 
|}
 
|}
 
</div>
 
</div>
  
 
== Substrate specificities ==
 
== Substrate specificities ==
The major activities reported for this family are alpha-L-arabinofuranosidases <cite>#1</cite>, endo-alpha-L-arabinanases (or endo-processive arabinanases) <cite>#2#3</cite> and beta-D-xylosidases <cite>#4</cite>. An enzyme with exo alpha1,3-galactanase has also been described <cite>#5</cite>. A significant number of enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. It is likely that the natural activity of these enzymes is conferred by the aglycone component of the substrate. Indeed, the arabionofuranosidase activities already reported target very different glycans. Thus, the Bacillus subtilis enzyme arabinoxylan alpha-L-arabinofuranohydrolase specifically removes arabinofuranose side chains that are linked either alpha1,2 or alpha1,3  to backbone xylose residues <cite>#6</cite>, while the arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis will remove an alpha1,3-linked arabinofuranose from xylans where the xylose residue is substituted at both alpha1,2 and alpha1,3  with arabinose <cite>#7</cite>. By contrast some arabinofuranosidases are exo-alpha1,5-L-arabinanases <cite>#8</cite>. It should be noted that in several plant cell wall degrading organisms there has been a dramatic expansion in GH43 family enzymes, which may reflect a more extensive range of specificities than described to date.
+
The major activities reported for this family of [[glycoside hydrolases]] are &alpha;-L-arabinofuranosidases <cite>Flipphi1993a</cite>, [[endo]]-&alpha;-L-arabinanases (or endo-processive arabinanases) <cite>McKie1997 Flipphi1993b</cite> and &beta;-D-xylosidases <cite>Shallom2005</cite> (for further details see: [[Absolute configuration: D/L nomenclature]]). An enzyme with [[exo]] &alpha;-1,3-galactanase has also been described <cite>Ichinose2005</cite>. A significant number of enzymes in this family display both &alpha;-L-arabinofuranosidase and &beta;-D-xylosidase activity using aryl-glycosides as substrates. It is likely that the natural activity of these enzymes is conferred by the leaving-group component of the substrate. Indeed, the arabionofuranosidase activities already reported target very different glycans. Thus, the ''Bacillus subtilis'' enzyme arabinoxylan &alpha;-L-arabinofuranohydrolase specifically removes arabinofuranose side chains that are linked either &alpha;-1,2 or &alpha;-1,3  to backbone xylose residues <cite>Bourgois2007</cite>, while the arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from ''Bifidobacterium adolescentis'' will remove an &alpha;-1,3-linked arabinofuranose from xylans where the xylose residue is substituted at both &alpha;-1,2 and &alpha;-1,3  with arabinose <cite>vandenBroek2005</cite>. By contrast some arabinofuranosidases are [[exo]]-&alpha;-1,5-L-arabinanases <cite>Matsuo2000</cite>. It should be noted that in several plant cell wall degrading organisms there has been a dramatic expansion in GH43 family enzymes, which may reflect a more extensive range of specificities than described to date.  In light of the sequence and functional diversity of GH43 members, this family has been divided into subfamilies <cite>Mewis2016</cite>.
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
NMR, deploying arabinan as the substrate, showed that an endo-alpha1,5-arabinanase displays a single displacement or inverting mechanism <cite>#2</cite>. The catalytic general base, an aspartate, the catalytic general acid, a glutamate, and an aspartate that modules the pKa of the general base were identified through the crystal structure of ''Cellvibrio japonicus'' CjAbn43A, and confirmed by site-directed mutagenesis. Further biochemical proof for the catalytic function of the equivalent residues in a beta-xylosidase were obtained by demonstrating a relationship between the activity of the catalytic acid and the pKa of the leaving group of the substrate. The identity of the catalytic base was achieved by azide rescue of a mutant of this ressidue <cite>#2</cite>.
+
NMR, deploying arabinan as the substrate, showed that an [[endo]]-&alpha;-1,5-arabinanase uses an [[inverting]] mechanism <cite>Pitson1996</cite>. However, the first demonstration of an inverting enzyme, which was later shown to be a GH43 &beta;-xylosidase, was by using a linked assay with an anomeric stereospecific D-xylose isomerase <cite>KerstersHilderson1976</cite>.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The identity of the catalytic residues have been identified, iniitially, by site-directed mutagenesis and subsequently through biochemical analysis. In contrast to many "inverting" glycoside hydrolases there appears to be a single candidate catalytic general base.
+
The catalytic [[general base]], an aspartate, the catalytic [[general acid]], a glutamate, and an aspartate that modules the p''K''<sub>a</sub> of the general acid were identified through the crystal structure of ''Cellvibrio japonicus'' CjAbn43A, and confirmed by site-directed mutagenesis <cite>Nurizzo2002</cite>. Further biochemical proof for the catalytic function of the equivalent residues in a &beta;-xylosidase were obtained by demonstrating a relationship between the activity of the catalytic acid and the p''K''<sub>a</sub> of the leaving group of the substrate. The identity of the catalytic base was achieved by azide rescue of a mutant of this residue <cite>Shallom2005</cite>. In contrast to many [[inverting]] [[glycoside hydrolases]] there appears to be a single candidate catalytic general base for the arabinofuranosidases and xylosidases in this family, but this residue is absent in GH43 galactosidase <cite>Jiang2012</cite>.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The GH43 enzymes display a 'non-velcroed' five-bladed-beta-propeller. The propeller is based upon a five-fold repeat of blades composed of four-stranded beta-sheets <cite>#8</cite>.  The substrate-binding surface of Arb43A is in a long surface depression, with the catalytic constellation of carboxylates at its center. The exo-processive activity of the enzyme is conferred by a subtle steric block at the +3 subsite explaining why the enzyme releases, exclusively, arabinotriose <cite>#9</cite>. In the arabinofuranosidases and xylosidases the active site comprises a deep pocket and the orientation of the substrate is very different between the enzymes, which contributes to the varied specificities observed across the GH43 landscape <cite>#10</cite>.
+
The GH43 enzymes display a 'non-velcroed' five-bladed-&beta;-propeller. The propeller is based upon a five-fold repeat of blades composed of four-stranded &beta;-sheets <cite>Nurizzo2002</cite>.  The substrate-binding surface of Arb43A is in a long surface depression, with the catalytic constellation of carboxylates at its center. The exo-processive activity of the enzyme is conferred by a subtle steric block at the +3 subsite explaining why the enzyme releases, exclusively, arabinotriose <cite>Proctor2005</cite>. In the arabinofuranosidases and xylosidases the active site comprises a deep pocket and the orientation of the substrate is very different between the enzymes, which contributes to the varied specificities observed across the GH43 landscape <cite>Vandermarliere2009 Brux2006</cite>.
  
 
== Family Firsts ==
 
== Family Firsts ==
;First sterochemistry determination:  
+
;First sterochemistry determination: Determined for the ''Bacillus pumilus'' &beta;-xylosidase using an anomeric specific D-xylose isomerase <cite>14</cite> and determined for an arabinanase by proton NMR <cite>Pitson1996</cite>.
;First catalytic nucleophile identification:  
+
;First general base residue identification: Based on mutagensis informed by 3D structural data <cite>Nurizzo2002</cite>
;First general acid/base residue identification:  
+
;First general acid residue identification: Based on mutagensis informed by 3D structural data <cite>Nurizzo2002</cite>
;First 3-D structure: alpha-L-Arabinanase from ''Cellvibrio japonicus'' <cite>1</cite>.
+
;First 3-D structure: &alpha;-L-arabinanase from ''Cellvibrio japonicus'' <cite>Nurizzo2002</cite>.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#1 pmid=12198486
+
#Flipphi1993a pmid=7764056
#2 pmid=8946944
+
#McKie1997 pmid=9163351
 +
#Flipphi1993b pmid=7764386
 +
#Shallom2005 pmid=15628881
 +
#Ichinose2005 pmid=15866877
 +
#Bourgois2007 pmid=17426966
 +
#vandenBroek2005 pmid=15650848
 +
#Matsuo2000 pmid=10657233
 +
#Pitson1996 pmid=8946944
 +
#Nurizzo2002 pmid=12198486
 +
#Proctor2005 pmid=15708971
 +
#Vandermarliere2009 pmid=18980579
 +
#Brux2006 pmid=16631196
 +
#KerstersHilderson1976 pmid=1268883
 +
#Jiang2012 pmid=22960181
 +
#Mewis2016 pmid=26729713
 +
 
 
</biblio>
 
</biblio>
 
+
[[Category:Glycoside Hydrolase Families|GH043]]
[[Category:Glycoside Hydrolase Families]]
 

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Glycoside Hydrolase Family GH43
Clan GH-F
Mechanism inverting
Active site residues Known
CAZy DB link
http://www.cazy.org/GH43.html

Substrate specificities

The major activities reported for this family of glycoside hydrolases are α-L-arabinofuranosidases [1], endo-α-L-arabinanases (or endo-processive arabinanases) [2, 3] and β-D-xylosidases [4] (for further details see: Absolute configuration: D/L nomenclature). An enzyme with exo α-1,3-galactanase has also been described [5]. A significant number of enzymes in this family display both α-L-arabinofuranosidase and β-D-xylosidase activity using aryl-glycosides as substrates. It is likely that the natural activity of these enzymes is conferred by the leaving-group component of the substrate. Indeed, the arabionofuranosidase activities already reported target very different glycans. Thus, the Bacillus subtilis enzyme arabinoxylan α-L-arabinofuranohydrolase specifically removes arabinofuranose side chains that are linked either α-1,2 or α-1,3 to backbone xylose residues [6], while the arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis will remove an α-1,3-linked arabinofuranose from xylans where the xylose residue is substituted at both α-1,2 and α-1,3 with arabinose [7]. By contrast some arabinofuranosidases are exo-α-1,5-L-arabinanases [8]. It should be noted that in several plant cell wall degrading organisms there has been a dramatic expansion in GH43 family enzymes, which may reflect a more extensive range of specificities than described to date. In light of the sequence and functional diversity of GH43 members, this family has been divided into subfamilies [9].

Kinetics and Mechanism

NMR, deploying arabinan as the substrate, showed that an endo-α-1,5-arabinanase uses an inverting mechanism [10]. However, the first demonstration of an inverting enzyme, which was later shown to be a GH43 β-xylosidase, was by using a linked assay with an anomeric stereospecific D-xylose isomerase [11].

Catalytic Residues

The catalytic general base, an aspartate, the catalytic general acid, a glutamate, and an aspartate that modules the pKa of the general acid were identified through the crystal structure of Cellvibrio japonicus CjAbn43A, and confirmed by site-directed mutagenesis [12]. Further biochemical proof for the catalytic function of the equivalent residues in a β-xylosidase were obtained by demonstrating a relationship between the activity of the catalytic acid and the pKa of the leaving group of the substrate. The identity of the catalytic base was achieved by azide rescue of a mutant of this residue [4]. In contrast to many inverting glycoside hydrolases there appears to be a single candidate catalytic general base for the arabinofuranosidases and xylosidases in this family, but this residue is absent in GH43 galactosidase [13].

Three-dimensional structures

The GH43 enzymes display a 'non-velcroed' five-bladed-β-propeller. The propeller is based upon a five-fold repeat of blades composed of four-stranded β-sheets [12]. The substrate-binding surface of Arb43A is in a long surface depression, with the catalytic constellation of carboxylates at its center. The exo-processive activity of the enzyme is conferred by a subtle steric block at the +3 subsite explaining why the enzyme releases, exclusively, arabinotriose [14]. In the arabinofuranosidases and xylosidases the active site comprises a deep pocket and the orientation of the substrate is very different between the enzymes, which contributes to the varied specificities observed across the GH43 landscape [15, 16].

Family Firsts

First sterochemistry determination
Determined for the Bacillus pumilus β-xylosidase using an anomeric specific D-xylose isomerase [17] and determined for an arabinanase by proton NMR [10].
First general base residue identification
Based on mutagensis informed by 3D structural data [12]
First general acid residue identification
Based on mutagensis informed by 3D structural data [12]
First 3-D structure
α-L-arabinanase from Cellvibrio japonicus [12].

References

  1. Flipphi MJ, Visser J, van der Veen P, and de Graaff LH. (1993). Cloning of the Aspergillus niger gene encoding alpha-L-arabinofuranosidase A. Appl Microbiol Biotechnol. 1993;39(3):335-40. DOI:10.1007/BF00192088 | PubMed ID:7764056 [Flipphi1993a]
  2. McKie VA, Black GW, Millward-Sadler SJ, Hazlewood GP, Laurie JI, and Gilbert HJ. (1997). Arabinanase A from Pseudomonas fluorescens subsp. cellulosa exhibits both an endo- and an exo- mode of action. Biochem J. 1997;323 ( Pt 2)(Pt 2):547-55. DOI:10.1042/bj3230547 | PubMed ID:9163351 [McKie1997]
  3. Flipphi MJ, Panneman H, van der Veen P, Visser J, and de Graaff LH. (1993). Molecular cloning, expression and structure of the endo-1,5-alpha-L-arabinase gene of Aspergillus niger. Appl Microbiol Biotechnol. 1993;40(2-3):318-26. DOI:10.1007/BF00170387 | PubMed ID:7764386 [Flipphi1993b]
  4. Shallom D, Leon M, Bravman T, Ben-David A, Zaide G, Belakhov V, Shoham G, Schomburg D, Baasov T, and Shoham Y. (2005). Biochemical characterization and identification of the catalytic residues of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6. Biochemistry. 2005;44(1):387-97. DOI:10.1021/bi048059w | PubMed ID:15628881 [Shallom2005]
  5. Ichinose H, Yoshida M, Kotake T, Kuno A, Igarashi K, Tsumuraya Y, Samejima M, Hirabayashi J, Kobayashi H, and Kaneko S. (2005). An exo-beta-1,3-galactanase having a novel beta-1,3-galactan-binding module from Phanerochaete chrysosporium. J Biol Chem. 2005;280(27):25820-9. DOI:10.1074/jbc.M501024200 | PubMed ID:15866877 [Ichinose2005]
  6. Bourgois TM, Van Craeyveld V, Van Campenhout S, Courtin CM, Delcour JA, Robben J, and Volckaert G. (2007). Recombinant expression and characterization of XynD from Bacillus subtilis subsp. subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase. Appl Microbiol Biotechnol. 2007;75(6):1309-17. DOI:10.1007/s00253-007-0956-2 | PubMed ID:17426966 [Bourgois2007]
  7. van den Broek LA, Lloyd RM, Beldman G, Verdoes JC, McCleary BV, and Voragen AG. (2005). Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083. Appl Microbiol Biotechnol. 2005;67(5):641-7. DOI:10.1007/s00253-004-1850-9 | PubMed ID:15650848 [vandenBroek2005]
  8. Matsuo N, Kaneko S, Kuno A, Kobayashi H, and Kusakabe I. (2000). Purification, characterization and gene cloning of two alpha-L-arabinofuranosidases from streptomyces chartreusis GS901. Biochem J. 2000;346 Pt 1(Pt 1):9-15. | Google Books | Open Library PubMed ID:10657233 [Matsuo2000]
  9. Mewis K, Lenfant N, Lombard V, and Henrissat B. (2016). Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization. Appl Environ Microbiol. 2016;82(6):1686-1692. DOI:10.1128/AEM.03453-15 | PubMed ID:26729713 [Mewis2016]
  10. Pitson SM, Voragen AG, and Beldman G. (1996). Stereochemical course of hydrolysis catalyzed by arabinofuranosyl hydrolases. FEBS Lett. 1996;398(1):7-11. DOI:10.1016/s0014-5793(96)01153-2 | PubMed ID:8946944 [Pitson1996]
  11. Kersters-Hilderson H, Claeyssens M, van Doorslaer E, and de Bruyne CK. (1976). Determination of the anomeric configuration of D-xylose with D-xylose isomerases. Carbohydr Res. 1976;47(2):269-73. DOI:10.1016/s0008-6215(00)84192-0 | PubMed ID:1268883 [KerstersHilderson1976]
  12. Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, and Davies GJ. (2002). Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Nat Struct Biol. 2002;9(9):665-8. DOI:10.1038/nsb835 | PubMed ID:12198486 [Nurizzo2002]
  13. Jiang D, Fan J, Wang X, Zhao Y, Huang B, Liu J, and Zhang XC. (2012). Crystal structure of 1,3Gal43A, an exo-β-1,3-galactanase from Clostridium thermocellum. J Struct Biol. 2012;180(3):447-57. DOI:10.1016/j.jsb.2012.08.005 | PubMed ID:22960181 [Jiang2012]
  14. Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, and Gilbert HJ. (2005). Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A. 2005;102(8):2697-702. DOI:10.1073/pnas.0500051102 | PubMed ID:15708971 [Proctor2005]
  15. Vandermarliere E, Bourgois TM, Winn MD, van Campenhout S, Volckaert G, Delcour JA, Strelkov SV, Rabijns A, and Courtin CM. (2009). Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family. Biochem J. 2009;418(1):39-47. DOI:10.1042/BJ20081256 | PubMed ID:18980579 [Vandermarliere2009]
  16. Brüx C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, and Schomburg D. (2006). The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues. J Mol Biol. 2006;359(1):97-109. DOI:10.1016/j.jmb.2006.03.005 | PubMed ID:16631196 [Brux2006]

All Medline abstracts: PubMed