Flexibility and specificity of the cohesin–dockerin interaction: implications for cellulosome assembly and functionality

Artificial scaffolds for enhanced biocatalysis

Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to colocalize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.

Combined Crystal Structure of a Type I Cohesin: MUTATION AND AFFINITY BINDING STUDIES REVEAL STRUCTURAL DETERMINANTS OF COHESIN-DOCKERIN SPECIFICITIES

Cohesin-dockerin interactions orchestrate the assembly of one of nature's most elaborate multienzyme complexes, the cellulosome. Cellulosomes are produced exclusively by anaerobic microbes and mediate highly efficient hydrolysis of plant structural polysaccharides, such as cellulose and hemicellulose. In the canonical model of cellulosome assembly, type I dockerin modules of the enzymes bind to reiterated type I cohesin modules of a primary scaffoldin. Each type I dockerin contains two highly conserved cohesin-binding sites, which confer quaternary flexibility to the multienzyme complex. The scaffoldin also bears a type II dockerin that anchors the entire complex to the cell surface by binding type II cohesins of anchoring scaffoldins. In Bacteroides cellulosolvens, however, the organization of the cohesin-dockerin types is reversed, whereby type II cohesin-dockerin pairs integrate the enzymes into the primary scaffoldin, and type I modules mediate cellulosome attachment to an anchoring scaffoldin. Here, we report the crystal structure of a type I cohesin from B. cellulosolvens anchoring scaffoldin ScaB to 1.84-Å resolution. The structure resembles other type I cohesins, and the putative dockerin-binding site, centered at β-strands 3, 5, and 6, is likely to be conserved in other B. cellulosolvens type I cohesins. Combined computational modeling, mutagenesis, and affinity-based binding studies revealed similar hydrogen-bonding networks between putative Ser/Asp recognition residues in the dockerin at positions 11/12 and 45/46, suggesting that a dual-binding mode is not exclusive to the integration of enzymes into primary cellulosomes but can also characterize polycellulosome assembly and cell-surface attachment. This general approach may provide valuable structural information of the cohesin-dockerin interface, in lieu of a definitive crystal structure.

Purification, crystallization and preliminary X-ray characterization of the third ScaB cohesin in complex with an ScaA X-dockerin from Acetivibrio cellulolyticus

Interactions between cohesin and dockerin modules are critical for the formation of the cellulosome, which is responsible for the efficient degradation of plant cell-wall carbohydrates by anaerobes. Type I dockerin modules found in modular enzymatic components interact with type I cohesins in primary scaffoldins, enabling the assembly of the multi-enzyme complex. In contrast, type II dockerins located in primary scaffoldins bind to type II cohesins in adaptor scaffoldins or anchoring scaffoldins located at the bacterial envelope, contributing to the cell-surface attachment of the entire complex. Acetivibrio cellulolyticus possesses an extremely complex cellulosome arrangement which is organized by a primary enzyme-binding scaffoldin (ScaA), two anchoring scaffoldins (ScaC and ScaD) and an unusual adaptor scaffoldin (ScaB). An ScaA X-dockerin mutated to inactivate one of the two putative cohesin-binding interfaces complexed with the third ScaB cohesin from A. cellulolyticus has been purified and crystallized and data were collected to a resolution of 2.41 Å.

Purification, crystallization and preliminary X-ray characterization of the Acetivibrio cellulolyticus type I cohesin ScaC in complex with the ScaB dockerin

The cellulosome, a highly elaborate extracellular multi-enzyme complex of cellulases and hemicellulases, is responsible for the efficient degradation of plant cell-wall carbohydrates by anaerobic microorganisms. Cohesin and dockerin recognition pairs are integral to the architecture of the cellulosome. Thus, type I cohesin:dockerins are important for attaching the modular enzymatic components to primary scaffoldins to form the cellulosome. In contrast, type II dockerins located in primary scaffoldins bind to anchoring scaffoldins, thus contributing to the cell-surface attachment of the entire complex. Since anchoring scaffoldins usually contain more than one type II cohesin, they contribute to the assembly of polycellulosomes. Acetivibrio cellulolyticus possesses an extremely complex cellulosome arrangement which is organized by a primary enzyme-binding scaffoldin (ScaA), two anchoring scaffoldins (ScaC and ScaD) and an unusual adaptor scaffoldin (ScaB). A ScaB dockerin mutated to inactivate one of the two putative cohesin-binding interfaces complexed with the ScaC cohesin from A. cellulolyticus has been purified and crystallized and data were collected from tetragonal and monoclinic crystal forms to resolutions of 1.5 and 6.0 Å, respectively.