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Difference between revisions of "Template:CBMFamilyPage"
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− | < | + | <noinclude> |
− | + | <blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;"> | |
+ | '''The text below is a template to help CAZypedians create a consistent layout for [[Carbohydrate Binding Module Families|CBM]] family entries.''' It can be [http://www.mediawiki.org/wiki/Transclusion transcluded] into ''new'' pages via a drop-down menu provided by the [[Special:Boilerplates|MultiBoilerplate extension]] installed on ''CAZypedia''. | ||
+ | </blockquote> | ||
+ | ---- | ||
+ | </noinclude> | ||
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
− | < | + | <includeonly>{{UnderConstruction}}</includeonly> |
− | * [[Author]]: | + | * [[Author]]: [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]] |
− | * [[Responsible Curator]]: | + | * [[Responsible Curator]]: [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]] |
---- | ---- | ||
− | < | + | <!-- The data in the table below should be updated by the Author/Curator according to current information on the family --> |
− | '' | + | <div style="float:right"> |
− | < | + | {| {{Prettytable}} |
+ | |- | ||
+ | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
+ | |- | ||
+ | | colspan="2" |{{CAZyDBlink}}CBMnn.html | ||
+ | |} | ||
+ | </div> | ||
+ | <!-- This is the end of the table --> | ||
== Ligand specificities == | == Ligand specificities == | ||
Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant. | Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant. | ||
+ | |||
+ | ''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010 Armenta2017</cite>. | ||
== Structural Features == | == Structural Features == | ||
− | + | ''Content in this section should include, in paragraph form, a description of:'' | |
− | Structural fold (beta trefoil, beta sandwich, etc.) | + | * '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.) |
− | + | * '''Type:''' Include here Type A, B, or C and properties | |
− | Include here Type A, B, or C and properties | + | * '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. |
− | |||
− | |||
− | Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. | ||
== Functionalities == | == Functionalities == | ||
− | + | ''Content in this section should include, in paragraph form, a description of:'' | |
− | Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate. | + | * '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate. |
− | + | * '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.) | |
− | 1. Glycoside Hydrolase Activity | + | * '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc. |
− | |||
− | 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.) | ||
− | |||
− | Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc. | ||
== Family Firsts == | == Family Firsts == | ||
− | + | ;First Identified | |
− | + | :Insert archetype here, possibly including ''very brief'' synopsis. | |
− | + | ;First Structural Characterization | |
− | + | :Insert archetype here, possibly including ''very brief'' synopsis. | |
== References == | == References == | ||
<biblio> | <biblio> | ||
#Cantarel2009 pmid=18838391 | #Cantarel2009 pmid=18838391 | ||
− | #DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. | + | #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/BIO03004026 DOI:10.1042/BIO03004026]. |
#Boraston2004 pmid=15214846 | #Boraston2004 pmid=15214846 | ||
#Hashimoto2006 pmid=17131061 | #Hashimoto2006 pmid=17131061 | ||
#Shoseyov2006 pmid=16760304 | #Shoseyov2006 pmid=16760304 | ||
#Guillen2010 pmid=19908036 | #Guillen2010 pmid=19908036 | ||
+ | #Armenta2017 pmid=28547780 | ||
</biblio> | </biblio> | ||
− | < | + | <!-- Do not delete this Category tag --> |
+ | <includeonly>[[Category:Carbohydrate Binding Module Families|CBMnnn]]</includeonly> | ||
+ | <!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. --> |
Latest revision as of 12:27, 4 July 2023
The text below is a template to help CAZypedians create a consistent layout for CBM family entries. It can be transcluded into new pages via a drop-down menu provided by the MultiBoilerplate extension installed on CAZypedia.
CAZy DB link | |
http://www.cazy.org/CBMnn.html |
Ligand specificities
Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.
Note: Here is an example of how to insert references in the text, together with the "biblio" section below: Please see these references for an essential introduction to the CAZy classification system: [1, 2]. CBMs, in particular, have been extensively reviewed [3, 4, 5, 6, 7].
Structural Features
Content in this section should include, in paragraph form, a description of:
- Fold: Structural fold (beta trefoil, beta sandwich, etc.)
- Type: Include here Type A, B, or C and properties
- Features of ligand binding: Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.
Functionalities
Content in this section should include, in paragraph form, a description of:
- Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
- Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
- Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.
Family Firsts
- First Identified
- Insert archetype here, possibly including very brief synopsis.
- First Structural Characterization
- Insert archetype here, possibly including very brief synopsis.
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. DOI:10.1042/BIO03004026.
- 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 |
- Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
- Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
- Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
- Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |
- Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, and Rodríguez-Sanoja R. (2017). Advances in molecular engineering of carbohydrate-binding modules. Proteins. 2017;85(9):1602-1617. DOI:10.1002/prot.25327 |