7CBD

Catalytic domain of Cellulomonas fimi Cel6B

Summary for 7CBD

• Entry DOI: 10.2210/pdb7cbd/pdb
• Descriptor: Exoglucanase A (2 entities in total)
• Functional Keywords: cellulase, hydrolase
• Biological source: Cellulomonas fimi (strain ATCC 484 / DSM 20113 / JCM 1341 / NBRC 15513 / NCIMB 8980 / NCTC 7547)
• Total number of polymer chains: 1
• Total formula weight: 49162.41

Authors

Nakamura, A.,Ishiwata, D.,Visootsat, A.,Uchiyama, T.,Mizutani, K.,Kaneko, S.,Murata, T.,Igarashi, K.,Iino, R. (deposition date: 2020-06-12, release date: 2020-08-26, Last modification date: 2024-10-30)

Primary citation

Nakamura, A.,Ishiwata, D.,Visootsat, A.,Uchiyama, T.,Mizutani, K.,Kaneko, S.,Murata, T.,Igarashi, K.,Iino, R.
Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases.
J.Biol.Chem., 295:14606-14617, 2020

PubMed Abstract: Cellobiohydrolases directly convert crystalline cellulose into cellobiose and are of biotechnological interest to achieve efficient biomass utilization. As a result, much research in the field has focused on identifying cellobiohydrolases that are very fast. Cellobiohydrolase A from the bacterium (CfCel6B) and cellobiohydrolase II from the fungus (TrCel6A) have similar catalytic domains (CDs) and show similar hydrolytic activity. However, TrCel6A and CfCel6B have different cellulose-binding domains (CBDs) and linkers: TrCel6A has a glycosylated peptide linker, whereas CfCel6B's linker consists of three fibronectin type 3 domains. We previously found that TrCel6A's linker plays an important role in increasing the binding rate constant to crystalline cellulose. However, it was not clear whether CfCel6B's linker has similar function. Here we analyze kinetic parameters of CfCel6B using single-molecule fluorescence imaging to compare CfCel6B and TrCel6A. We find that CBD is important for initial binding of CfCel6B, but the contribution of the linker to the binding rate constant or to the dissociation rate constant is minor. The crystal structure of the CfCel6B CD showed longer loops at the entrance and exit of the substrate-binding tunnel compared with TrCel6A CD, which results in higher processivity. Furthermore, CfCel6B CD showed not only fast surface diffusion but also slow processive movement, which is not observed in TrCel6A CD. Combined with the results of a phylogenetic tree analysis, we propose that bacterial cellobiohydrolases are designed to degrade crystalline cellulose using high-affinity CBD and high-processivity CD.

PubMed: 32816991
DOI: 10.1074/jbc.RA120.014792

Experimental method

X-RAY DIFFRACTION (1.3 Å)