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Difference between revisions of "Template:CBMFamilyPage"

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<!-- The text below is a template to help you create a consistent layout for CBM family entries. Make sure to delete this comment at some point after the page is set up! -->
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<noinclude>
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<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
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'''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''.
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</blockquote>
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----
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</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 -->
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<nowiki>{{UnderConstruction}}</nowiki> <!-- REMOVE THESE nowiki TAGS BEFORE SAVING THE PAGE THE FIRST TIME. They prevent this Template page from showing-up in the list of pages "Under Construction" -->
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<includeonly>{{UnderConstruction}}</includeonly>
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* [[Author]]: ^^^Alicia Lammerts van Bueren^^^
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* [[Author]]: [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]
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* [[Responsible Curator]]:  ^^^Alicia Lammerts van Bueren^^^
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* [[Responsible Curator]]:  [[User:Elizabeth Ficko-Blean|Elizabeth Ficko-Blean]]
 
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<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
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<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
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''Page content has yet to be added.  In the meantime, 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</cite>.''
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{| {{Prettytable}}
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|-
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
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|-
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| colspan="2" |{{CAZyDBlink}}CBMnn.html
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|}
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</div>
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<!-- This is the end of the table -->
  
 
== Ligand specificities ==
 
== Ligand specificities ==
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Mention here all major ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here (such as BhCBM6 binding xylobiose and laminarihexaose).  
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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.
 +
 
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''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 ==
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===Fold===
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''Content in this section should include, in paragraph form, a description of:''
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Include here Type A, B, or C, fold (beta trefoil, beta sandwich most likely),
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* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
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* '''Type:''' Include here Type A, B, or C and properties
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===Properties of ligand binding===
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* '''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.
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What face of the CBM is the binding pocket located? Side or apex? Include examples pdb codes. important residues for binding (W, Y, F, subsites). Metal ion dependent?
 
  
 
== Functionalities ==  
 
== Functionalities ==  
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===Functional role of CBM===
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''Content in this section should include, in paragraph form, a description of:''
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Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
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* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
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===Most Common Associated Modules===
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* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
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1. Glycoside Hydrolase Activity
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* '''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.
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2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
 
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===Novel Applications===
 
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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 ==
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===First Identified===
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;First Identified
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insert text here
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:Insert archetype here, possibly including ''very brief'' synopsis.
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===First Structural Characterization===
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;First Structural Characterization
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insert text here
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:Insert archetype here, possibly including ''very brief'' synopsis.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 
#Cantarel2009 pmid=18838391
 
#Cantarel2009 pmid=18838391
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#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
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#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
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#Armenta2017 pmid=28547780
 
</biblio>
 
</biblio>
  
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<nowiki>[[Category:Carbohydrate Binding Module Families|CBMnnn]]</nowiki> <!-- REMOVE THESE nowiki TAGS BEFORE SAVING THE PAGE THE FIRST TIME. They prevent this Template page from showing-up in the list of CBM Family pages -->
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<!-- Do not delete this Category tag -->
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<includeonly>[[Category:Carbohydrate Binding Module Families|CBMnnn]]</includeonly>
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<!-- 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 11:27, 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
https://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

  1. 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.

    [DaviesSinnott2008]
  2. 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 | PubMed ID:18838391 [Cantarel2009]
  3. 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 | PubMed ID:15214846 [Boraston2004]
  4. 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 | PubMed ID:17131061 [Hashimoto2006]
  5. 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 | PubMed ID:16760304 [Shoseyov2006]
  6. 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 | PubMed ID:19908036 [Guillen2010]
  7. 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 | PubMed ID:28547780 [Armenta2017]

All Medline abstracts: PubMed


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