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Difference between revisions of "Polysaccharide Lyase Family 38"
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| Line 13: | Line 13: | ||
|'''3D structure''' | |'''3D structure''' | ||
| | | | ||
| − | + | ( α / α )<sub>7</sub> barrel | |
| − | |||
| − | |||
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
| | | | ||
| + | β-elimination | ||
|- | |- | ||
|'''Charge neutralizer''' | |'''Charge neutralizer''' | ||
| Line 24: | 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 33: | Line 32: | ||
<!-- This is the end of the table --> | <!-- This is the end of the table --> | ||
| + | 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: <cite>DaviesSinnott2008 Cantarel2009</cite>. | ||
== Substrate specificities == | == Substrate specificities == | ||
Content is to be added here. | Content is to be added here. | ||
| − | |||
| − | |||
| − | |||
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| Line 51: | Line 49: | ||
== Family Firsts == | == Family Firsts == | ||
| − | ;First | + | ;First description of catalytic activity: |
| − | ;First catalytic | + | *(1,4)-β-D-glucuronan activity by ''Brevundimonas sp. SH203'' cellouronate lyase (CUL-I) <cite> kikuchi2019 </cite>. |
| − | ;First | + | *Sodium-alginate, poly-mannuronate and poly-guluronate activity by ''Agarivorans sp. B2Z047'' alginate lyase (Aly38A) <cite> Sun2022 </cite>. |
| − | ;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]). | + | ;First catalytic base/acid: Content is to be added here. |
| + | ;First charge neutralizer: Content is to be added here. | ||
| + | ;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]) [No associated publication]. | ||
== 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 | ||
| + | |||
#kikuchi2019 pmid=31546007 | #kikuchi2019 pmid=31546007 | ||
| + | |||
#Pilgaard2022 pmid=34705548 | #Pilgaard2022 pmid=34705548 | ||
#Sun2022 pmid=35447927 | #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]] | ||
Latest revision as of 02:42, 4 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 | |
| https://www.cazy.org/PL38.html | |
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].
Substrate specificities
Content is to be added here.
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 description of catalytic activity
- (1,4)-β-D-glucuronan activity by Brevundimonas sp. SH203 cellouronate lyase (CUL-I) [3].
- Sodium-alginate, poly-mannuronate and poly-guluronate activity by Agarivorans sp. B2Z047 alginate lyase (Aly38A) [4].
- First catalytic base/acid
- Content is to be added here.
- First charge neutralizer
- 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) [No associated publication].
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 |
- 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 |
- 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 |
- 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 |