5FRE

Characterization of a novel CBM from Clostridium perfringens

Summary for 5FRE

• Entry DOI: 10.2210/pdb5fre/pdb
• Related: 5FRA
• Descriptor: EXO-ALPHA-SIALIDASE, N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: hydrolase, cbm40
• Biological source: CLOSTRIDIUM PERFRINGENS
• Total number of polymer chains: 3
• Total formula weight: 68609.13

Authors

Ribeiro, J.,Pau, W.,Pifferi, C.,Renaudet, O.,Varrot, A.,Mahal, L.K.,Imberty, A. (deposition date: 2015-12-17, release date: 2016-07-20, Last modification date: 2024-01-10)

Primary citation

Ribeiro, J.P.,Pau, W.,Pifferi, C.,Renaudet, O.,Varrot, A.,Mahal, L.K.,Imberty, A.
Characterization of a High-Affinity Sialic Acid-Specific Cbm40 from Clostridium Perfringens and Engineering of a Divalent Form.
Biochem.J., 473:2109-, 2016

PubMed Abstract: CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens Glycan arrays revealed its preference towards α(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to α(2,3)-sialyl-lactose with a Kd of ∼30 μM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form of the CBM, and using SPR (surface plasmon resonance) we have observed 6-11-fold binding increases due to the avidity affect. The structures of the CBM, resolved by X-ray crystallography, in complex with α(2,3)- or α(2,6)-sialyl-lactose explain its binding specificity and unusually strong binding.

PubMed: 27208171
DOI: 10.1042/BCJ20160340

Experimental method

X-RAY DIFFRACTION (1.9 Å)