4V1B

Structure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1 collected at the Zn edge

Summary for 4V1B

• Entry DOI: 10.2210/pdb4v1b/pdb
• Related: 4V17 4V18 4V1I
• Descriptor: CARBOHYDRATE BINDING MODULE (2 entities in total)
• Functional Keywords: sugar binding protein, cellulosome
• Biological source: RUMINOCOCCUS FLAVEFACIENS
• Total number of polymer chains: 2
• Total formula weight: 34546.37

Authors

Venditto, I.,Centeno, M.S.J.,Ferreira, L.M.A.,Fontes, C.M.G.A.,Najmudin, S. (deposition date: 2014-09-25, release date: 2016-01-20, Last modification date: 2024-01-10)

Primary citation

Venditto, I.,Luis, A.S.,Rydahl, M.,Schuckel, J.,Fernandes, V.O.,Vidal-Melgosa, S.,Bule, P.,Goyal, A.,Pires, V.M.R.,Dourado, C.G.,Ferreira, L.M.A.,Coutinho, P.M.,Henrissat, B.,Knox, J.P.,Basle, A.,Najmudin, S.,Gilbert, H.J.,Willats, W.G.T.,Fontes, C.M.G.A.
Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects an Expansion in Glycan Recognition.
Proc.Natl.Acad.Sci.USA, 113:7136-, 2016

PubMed Abstract: The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens The data identified six previously unidentified CBM families that targeted β-glucans, β-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize β-glucans and β-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose.

PubMed: 27298375
DOI: 10.1073/PNAS.1601558113

Experimental method

X-RAY DIFFRACTION (2.69 Å)