Difference between revisions of "Carbohydrate Binding Module Family 78"

Revision as of 14:02, 19 February 2018

Ligand specificities

CBM78 is a family identified in the Ruminococcus flavefaciens cellulosome, a ruminal cellulolytic bacterium (1). CBM78 is a component of an enzyme that contains a catalytic module derived from GH5_4 and displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans. CBM78 also binds galactomannan and contains a GH26 “β1,4-mannanase” catalytic module (2). CBM78_GH5 displays highest affinity for xyloglucan. The similar affinity of CBM78_GH5 for cellohexaose and cellopentaose suggests five dominant sugar binding sites. The higher affinity of CBM78GH5 for XXXG than Cellotetraose, suggests a recognition of the xylose side chains. No binding to regenerated (noncrystalline) insoluble cellulose (RC) is detected.

Structural Features

The structure of CBM78_RfGH5 was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 2.0 Å. CBM78_RfGH5 has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) (2). β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Trp496, Trp554, Tyr555, and Phe479 are aligned along the cleft. This hydrophobic region is the glucan binding site in CBM78_RfGH5 (2).

Functionalities

CBM78 plays an enzyme-targeting role that is specific to Ruminococcus and a contribution to enzyme function in a highly complex scaffolding. CBM78 that binds β-glucans is component of enzyme that contains catalytic modules derived from GH5_4 with endo-β1,4-glucanases activity. CBM78 is also component of enzyme that contains catalytic modules derived from GH26 with β1,4-mannanase activity. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition of CBM78RfGH5. Alanine substitution of Trp496 or Trp554 in CBM78_RfGH5, which are conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants F479A and Y555A bound to xyloglucan, but not to barley β-glucan or HEC.The variant Q552A recognized xyloglucan and barley β-glucan, but not HEC. No binding to regenerated (noncrystalline) insoluble cellulose is detected and it is explained by the narrow binding cleft of CBM78_RfGH5.The mutagenesis data show that different residues play distinct roles in ligand recognition, explaining why this CBM can bind to a range of β-glucans.

Family Firsts

First Identified

CBM78 from the Ruminococcus flavefaciens CBM78_RfGH5 and CBM78_RfGH26 .

First Structural Characterization

The first available crystal structure and the first complex structure of a CBM78 is from CBM78_RfGH5.

References

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]
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. Download PDF version.
[DaviesSinnott2008]
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]
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]
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]
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]
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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-* [[Author]]: ^^^Immacolata Venditto^^^
-* [[Responsible Curator]]:  ^^^Harry Gilbert^^^
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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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-{| {{Prettytable}}
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-|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
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-| colspan="2" |{{CAZyDBlink}}CBM78.html
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 == 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.
+CBM78 is a family identified in the ''Ruminococcus flavefaciens'' cellulosome, a ruminal cellulolytic bacterium (1). CBM78 is a component of an enzyme that contains a catalytic module derived from GH5_4  and displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans. CBM78 also binds galactomannan and contains a GH26 “β1,4-mannanase” catalytic module (2). CBM78<sub>GH5</sub> displays highest affinity for xyloglucan. The similar affinity of CBM78<sub>GH5</sub> for cellohexaose and cellopentaose suggests five dominant sugar binding sites. The higher affinity of CBM78GH5  for XXXG than Cellotetraose, suggests a recognition of the xylose side chains. No binding to regenerated (noncrystalline) insoluble cellulose (RC) is detected.
-''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 ==
-''Content in this section should include, in paragraph form, a description of:''
+The structure of CBM78<sub>RfGH5</sub> was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 2.0 Å. CBM78<sub>RfGH5</sub> has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) (2). β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Trp496, Trp554, Tyr555, and Phe479 are aligned along the cleft. This hydrophobic region is the glucan binding site in CBM78<sub>RfGH5</sub> (2).
-* '''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:''
+CBM78 plays an enzyme-targeting role that is specific to Ruminococcus and a contribution to enzyme function in a highly complex scaffolding. CBM78 that binds β-glucans is component of enzyme that contains catalytic modules derived from GH5_4 with endo-β1,4-glucanases activity. CBM78 is also component of enzyme that contains catalytic modules derived from GH26 with β1,4-mannanase activity. Mutagenesis experiments confirmed the importance of the aromatic residues in ligand recognition of CBM78RfGH5. Alanine substitution of Trp496 or Trp554 in CBM78<sub>RfGH5</sub>, which are conserved in the CBM family, resulted in complete loss of binding to all ligands. The mutants F479A and Y555A bound to xyloglucan, but not to barley β-glucan or HEC.The variant Q552A recognized xyloglucan and barley β-glucan, but not HEC. No binding to regenerated (noncrystalline) insoluble cellulose is detected and it is explained by the narrow binding cleft of CBM78<sub>RfGH5</sub>.The mutagenesis data show that different residues play distinct roles in ligand recognition, explaining why this CBM can bind to a range of β-glucans.
-* '''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.
+CBM78 from the ''Ruminococcus flavefaciens'' CBM78<sub>RfGH5</sub> and CBM78<sub>RfGH26</sub> .
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+The first available crystal structure and the first complex structure of a CBM78 is from CBM78<sub>RfGH5</sub>.
 == References ==