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 See a page that's out-of-date and just needs a touch-up?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 "Polysaccharide Lyase Family 20"
Harry Brumer (talk | contribs) (Created page with " <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> {{UnderConstruc...") |
|||
| Line 16: | Line 16: | ||
|- | |- | ||
|'''Metal Cofactor''' | |'''Metal Cofactor''' | ||
| − | | | + | |calcium |
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |unknown |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 29: | Line 29: | ||
== Substrate specificities == | == Substrate specificities == | ||
| − | + | Polysaccharide lyases of family 20 cleave &beta-1,4 linkages in polyglucuronate (&beta-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus ''Trichoderma reesei'' (TrGL) <cite>Konno2009a</cite>. TrGL was highly specific for &beta-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO) mediated oxidation (cellouronate). | |
| − | |||
| − | |||
| − | |||
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | A PL20 enzyme, TrGL, has been characterized as a &beta-1,4-glucuronan lyase. TrGL catalyzed depolymerization of &beta-1,4-glucuronan endolytically by &beta-elimination <cite>Konno2009a</cite> The enzyme was most active at pH 6.5 and 50 °C, and its activity and thermostability increased in the presence of calcium ions. | |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | There are approximately 40 completely conserved amino-acid residues in the PL20 members <cite>Konno2009b</cite> Possible catalytic residues has been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ <cite>Konno2009b</cite> <cite>Ogura2008</cite>. It seemed to be that the charge neutralizer, the catalytic base and the catalytic acid in the TrGL are Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required. | |
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | The structure of the TrGL was the first PL20 structure to be reported <cite>Konno2009b</cite>. TrGL has a typical &beta-jelly roll fold (2ZZJ, 1.8 Å). | |
== Family Firsts == | == Family Firsts == | ||
| − | ;First | + | ;First First catalytic activity: TrGl from ''Trichoderma reesei'' <cite>Konno2009a</cite> |
| − | + | ;First 3-D structure: TrGl from ''Trichoderma reesei'' <cite>Konno2009b</cite> | |
| − | |||
| − | ;First 3-D structure: | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Konno2009a pmid=18978091 |
| − | # | + | #Konno2009b pmid=19306878 |
| + | #Ogura2008 pmid=18514736 | ||
</biblio> | </biblio> | ||
[[Category:Polysaccharide Lyase Families|PL020]] | [[Category:Polysaccharide Lyase Families|PL020]] | ||
Revision as of 03:03, 7 August 2014
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Naotake Konno^^^
- Responsible Curator: ^^^Shinya Fushinobu^^^
| Polysaccharide Lyase Family PL20 | |
| Mechanism | β-elimination |
| Metal Cofactor | calcium |
| Active site residues | unknown |
| CAZy DB link | |
| https://www.cazy.org/PL20.html | |
Substrate specificities
Polysaccharide lyases of family 20 cleave &beta-1,4 linkages in polyglucuronate (&beta-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus Trichoderma reesei (TrGL) [1]. TrGL was highly specific for &beta-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO) mediated oxidation (cellouronate).
Kinetics and Mechanism
A PL20 enzyme, TrGL, has been characterized as a &beta-1,4-glucuronan lyase. TrGL catalyzed depolymerization of &beta-1,4-glucuronan endolytically by &beta-elimination [1] The enzyme was most active at pH 6.5 and 50 °C, and its activity and thermostability increased in the presence of calcium ions.
Catalytic Residues
There are approximately 40 completely conserved amino-acid residues in the PL20 members [2] Possible catalytic residues has been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ [2] [3]. It seemed to be that the charge neutralizer, the catalytic base and the catalytic acid in the TrGL are Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required.
Three-dimensional structures
The structure of the TrGL was the first PL20 structure to be reported [2]. TrGL has a typical &beta-jelly roll fold (2ZZJ, 1.8 Å).
Family Firsts
- First First catalytic activity
- TrGl from Trichoderma reesei [1]
- First 3-D structure
- TrGl from Trichoderma reesei [2]
References
- Konno N, Igarashi K, Habu N, Samejima M, and Isogai A. (2009). Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family. Appl Environ Microbiol. 2009;75(1):101-7. DOI:10.1128/AEM.01749-08 |
- Konno N, Ishida T, Igarashi K, Fushinobu S, Habu N, Samejima M, and Isogai A. (2009). Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei. FEBS Lett. 2009;583(8):1323-6. DOI:10.1016/j.febslet.2009.03.034 |
- Ogura K, Yamasaki M, Mikami B, Hashimoto W, and Murata K. (2008). Substrate recognition by family 7 alginate lyase from Sphingomonas sp. A1. J Mol Biol. 2008;380(2):373-85. DOI:10.1016/j.jmb.2008.05.008 |