DEP domain

Abstract: 3D domain swapping is a mechanism for forming oligomeric proteins from their monomers. In 3D domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical protein chain. The result is an intertwined dimer or higher oligomer, with one domain of each subunit replaced by the identical domain from another subunit. The swapped "domain" can be as large as an entire tertiary globular domain, or as small as an alpha-helix or a strand of a beta-sheet. Examples of 3D domain swapping are reviewed that suggest domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers, and that domain swapping may serve as a mechanism for evolution of some oligomeric proteins. Domain-swapped proteins present examples of a single protein chain folding into two distinct structures.

Abstract: Many RNA-binding proteins of the nucleus and cytoplasm, including pre-mRNA-, mRNA-, snRNA-, and pre-rRNA-binding proteins, contain a putative RNAbinding domain of approximately 90 amino acids whose amino acid sequence is conserved from yeast to man. The most highly conserved motif within this RNAbinding domain is an octapeptide, termed the ribonucleoprotein consensus sequence {RNP-CSI, which is an identifying feature of this group of proteins. Frequently, these proteins contain several similar, but nonidentical, RNP-CS-type RNA-binding domains. All of these proteins also contain at least one auxiliary domain that is unique to each type of protein and most likely functions in protein-protein interactions. Many, if not all, of the RNP-CS-type proteins display binding preferences for specific RNA sequences, and several have been shown to interact with pre-mRNA sequences important for premRNA processing. Recent work has shown that the proteins encoded by several developmental loci in Drosophila and maize contain RNP-CS and, therefore, are most likely RNA-binding proteins. Here we provide an overview of the structural characteristics of these proteins and speculate on how the modular structure of RNP-CS-type RNA-binding proteins may facilitate their participation in pathways that regulate development at the post-transcriptional level.

Abstract: The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.