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 See a page that's out-of-date and just needs a touch-up?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 38"
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 --> {{UnderConstruct...") |
|||
| (3 intermediate revisions by the same user not shown) | |||
| Line 13: | Line 13: | ||
|'''3D structure''' | |'''3D structure''' | ||
| | | | ||
| + | ( α / α )<sub>7</sub> barrel | ||
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
| | | | ||
| + | β-elimination | ||
|- | |- | ||
|'''Charge neutralizer''' | |'''Charge neutralizer''' | ||
| Line 21: | Line 23: | ||
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |unknown |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 51: | Line 53: | ||
;First catalytic nucleophile identification: Content is to be added here. | ;First catalytic nucleophile identification: Content is to be added here. | ||
;First general acid/base residue identification: Content is to be added here. | ;First general acid/base residue identification: Content is to be added here. | ||
| − | ;First 3-D structure: | + | ;First 3-D structure: ''Bacteroides ovatus ATCC 8483'' PL38 (PDB [https://www.rcsb.org/structure/3NFV 3NFV] and [https://www.rcsb.org/structure/3NNB 3NNB]), published by the Joint Center for Structural Genomics ([http://www.jcsg.org JCSG]). |
== References == | == References == | ||
<biblio> | <biblio> | ||
| + | |||
| + | #DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026DOI:10.1042/BIO03004026]. | ||
#Cantarel2009 pmid=18838391 | #Cantarel2009 pmid=18838391 | ||
| − | # | + | |
| + | #kikuchi2019 pmid=31546007 | ||
| + | |||
| + | #Pilgaard2022 pmid=34705548 | ||
| + | #Sun2022 pmid=35447927 | ||
| + | #Ronne2023 pmid=37791757 | ||
| + | |||
| + | |||
</biblio> | </biblio> | ||
<!-- Do not delete this Category tag --> | <!-- Do not delete this Category tag --> | ||
[[Category:Polysaccharide Lyase Families|PL038]] | [[Category:Polysaccharide Lyase Families|PL038]] | ||
Revision as of 08:06, 3 June 2024
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.
| Polysaccharide Lyase Family 38 | |
| 3D structure |
( α / α )7 barrel |
| Mechanism |
β-elimination |
| Charge neutralizer | |
| Active site residues | unknown |
| CAZy DB link | |
| http://www.cazy.org/PL38.html | |
Substrate specificities
Content is to be added here.
Authors may get an idea of what to put in each field from Curator Approved Polysaccharide Lyase Families. (TIP: Right click with your mouse and open this link in a new browser window...)
In the meantime, please see these references for an essential introduction to the CAZy classification system: [1, 2].
Kinetics and Mechanism
Content is to be added here.
Catalytic Residues
Content is to be added here.
Three-dimensional structures
Content is to be added here.
Family Firsts
- First stereochemistry determination
- Content is to be added here.
- First catalytic nucleophile identification
- Content is to be added here.
- First general acid/base residue identification
- Content is to be added here.
- First 3-D structure
- Bacteroides ovatus ATCC 8483 PL38 (PDB 3NFV and 3NNB), published by the Joint Center for Structural Genomics (JCSG).
References
-
Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. [1].
- Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
- Kikuchi M, Konno N, Suzuki T, Fujii Y, Kodama Y, Isogai A, and Habu N. (2020). A bacterial endo-β-1,4-glucuronan lyase, CUL-I from Brevundimonas sp. SH203, belonging to a novel polysaccharide lyase family. Protein Expr Purif. 2020;166:105502. DOI:10.1016/j.pep.2019.105502 |
- Pilgaard B, Vuillemin M, Munk L, Holck J, Meier S, Wilkens C, and Meyer AS. (2022). Discovery of a Novel Glucuronan Lyase System in Trichoderma parareesei. Appl Environ Microbiol. 2022;88(1):e0181921. DOI:10.1128/AEM.01819-21 |
- Sun XK, Gong Y, Shang DD, Liu BT, Du ZJ, and Chen GJ. (2022). Degradation of Alginate by a Newly Isolated Marine Bacterium Agarivorans sp. B2Z047. Mar Drugs. 2022;20(4). DOI:10.3390/md20040254 |
- Rønne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, and Svensson B. (2023). Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate. Appl Environ Microbiol. 2023;89(10):e0118523. DOI:10.1128/aem.01185-23 |