Consequences of domain insertion on sequence-structure divergence in a superfold

Abstract

Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and capdomain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to α-helices flanking the central β-sheet and not to the domain-domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies. directed evolution | phosphoryl transferase | protein evolution | structural bioinformatics | HAD superfamily T he universe of protein structures is vast and diverse, yet these innumerable structures can be categorized into a finite number of folds (1). Ideally, the protein fold has a robust yet evolvable architecture to deliver chemistry, bind interaction partners, or provide scaffolding. A popular strategy for the acquisition of new function(s) is the topological alteration of the fold to provide a new evolutionary platform. More frequently, existing and stable scaffolds are elaborated to attain diversity that is due to accumulation of stochastic, independent, and near-neutral mutations in the protein sequence. In a large number of cases, the expansion of functional space has been achieved by the tandem fusion of two or three domains to form evolutionary modules known as supradomains (2). An analysis of catalytic domains fused to the nucleotide-binding Rossmann domain has revealed that the sequential order of their connections is conserved because each pairing arose from a single recombination event (3). Another common structural embellishment is that of domain insertion(s) into existing folds (4)-a strategy that is ubiquitous in all structural classes, i.e., all α, all β, α + β, and α/β (5). For example, members of the A, B, and Y DNA polymerase superfamilies, Rab geranylgeranyl transferase superfamily, and alcohol dehydrogenase superfamily have inserted different domains into the native fold to fine tun...

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family

“…However, several studies have shown that protein-protein interactions decrease evolutionary rates, partly by decreasing the fraction of surface-exposed residues (5-9, 45). Likewise, interactions with large capping domains in the haloalkanoate dehalogenase superfamily constrain the structural divergence of their Rossman-fold core domain (46). Our observation that the OSBS family, which is primarily composed of monomers, evolved at a faster rate than related, homomultimeric families is consistent with these studies.…”

Crystal structure of a lipin/Pah phosphatidic acid phosphatase

“…C1 cap domains are inserted after the β1 strand, while C2 cap domains are inserted after the β3 strand. In both cases, these cap domains reside above the HAD core and help form a structural pocket above the active site to generate substrate specificity 20,33 .…”

Biology, Mechanism, and Structure of Enzymes in the α- d -Phosphohexomutase Superfamily

“…It should also help correct the widespread functional misannotation of these enzymes in databases. This ambitious goal is now feasible using a combination of approaches such as high-throughput substrate profiling and bioinformatic analyses, as has been done with other enzyme families (Burroughs et al, 2006; Huang et al, 2015; Pandya et al, 2013). …”