Restriction systems play a role in establishing the epigenetic landscape of bacterial genomes and serve as a key line of defense against bacteriophage viruses. One of the best characterized restriction systems is McrBC, a modular, motor-driven endonuclease that targets and degrades foreign DNA. Canonical McrBC homologs are comprised of McrB, a DNA-binding AAA+ motor protein that assembles into asymmetric hexamers, and its partner endonuclease McrC, which cannot bind DNA alone and must associate with McrB oligomers to form a restriction complex. McrC’s interaction with McrB stimulates McrB’s basal GTP hydrolysis, which powers translocation on DNA substrates. McrB’s GTP specificity is mediated by the flexible N-linker region between its DNA-binding and AAA+ domains. Previous cryo-EM reconstructions were unable to clearly resolve the placement and orientation of DNA-binding domains on the AAA+ motor scaffold, which was likely due to conformational heterogeneity caused by the flexible N-linker. Distantly related McrBC homologs like Lactococcus lactis LlaI and Bacillus subtilis BsuMI lack a fused DNA-binding domain, with separate reading frames encoding their DNA-binding (R1) and AAA+ (R2) domains. The lack of a linker region in these noncanonical homologs suggests that 1) R1 and R2 must associate stably in the assembled complex and could therefore provide an amenable structural template for determining the pathway of DNA, and 2) there must be a unique mechanism for nucleotide specificity specific to this subset of the family. To investigate these hypotheses, I purified and solved the crystal structures of LlaI.R2 and LlaI.R1 to 1.80 Å and 1.52 Å, respectively. These crystal structures highlight the conservation of structural architecture and catalytic mechanism among the broader family, while revealing unique insights concerning the evolution of nucleotide specificity and the organization of DNA binding in McrBC restriction complexes. This thesis also includes a literature review on recombinant spider silk, with extensive discussion of its molecular structure, material properties, heterologous production in recombinant hosts, downstream applications, and industry landscape context, which I co-authored as a part of a student-run non-profit initiative to bridge the gaps between academia and industry.