We invest quite a bit of date looking at individual necessary protein family members towards goal to further our very own knowledge of their progression, structure and you may form.
Nitrogen regulatory (PII) proteins are signal transduction molecules involved in controlling nitrogen metabolism in prokaryots. PII proteins integrate the signals of intracellular nitrogen and carbon status into the control of enzymes involved in nitrogen assimilation. Using elaborate sequence similarity detection schemes, we show that five clusters of orthologs (COGs) and several small divergent protein groups belong to the PII superfamily and predict their structure to be a (???)2 ferredoxin-like fold. Proteins from the newly emerged PII superfamily are present in all major phylogenetic lineages. The PII homologs are quite diverse, with below random (as low as 1%) pairwise sequence identities between some members of distant groups. Despite this sequence diversity, evidence suggests that the different subfamilies retain the PII trimeric structure important for ligand-binding site formation and maintain a conservation of conservations at residue positions important for PII function. Because most of the orthologous groups within the PII superfamily are composed entirely of hypothetical proteins, our remote homology-based structure prediction provides the only information about them. Analogous to structural genomics efforts, such prediction gives clues to the biological roles of these proteins and allows us to hypothesize about locations of functional sites on model structures or rationalize about available experimental information. For instance, conserved residues in one of the families map in close proximity to each other on PII structure, allowing for a possible metal-binding site in the proteins coded by the locus known to affect sensitivity to divalent metal ions. Presented analysis pushes the limits of sequence similarity searches and exemplifies one of the extreme cases of reliable sequence-based structure prediction. In conjunction with structural genomics efforts to shed light on protein function, our strategies make it possible to detect homology between highly diverse sequences and are aimed at understanding the most remote evolutionary connections in the protein world. PDF
The fresh new O-linked GlcNAc transferases (OGTs) was a lately characterized band of largely eukaryotic nutrients you to include just one beta-N-acetylglucosamine moiety to particular serine otherwise threonine hydroxyls. Within the humans, this process are element of a sugar regulation mechanism or cellular signaling pathway that is employed in of several extremely important diseases, particularly diabetes, malignant tumors, and you may neurodegeneration. Although not, zero architectural facts about the human OGT is obtainable, except for the newest character from tetratricopeptide repeats (TPR) from the N terminus. This new urban centers from substrate joining internet is actually unknown and the architectural basis for that it enzyme’s form is not obvious. Here, secluded homology are stated involving the OGTs and you will a crowd out of varied sugar running minerals, in addition to healthy protein with known structure such as glycogen phosphorylase, UDP-GlcNAc dos-epimerase, in addition to glycosyl transferase MurG. A conserved theme from the next Rossmann domain items to new UDP-GlcNAc donor binding webpages. Which achievement is backed by a mixture of statistically significant PSI-Great time attacks, opinion secondary structure predictions, and a flex identification hit so you’re able to MurG. On top of that, iterative PSI-Blast databases hunt show that proteins homologous into OGTs means a huge and you may varied superfamily that is termed GPGTF (glycogen phosphorylase/glycosyl transferase). Around you to-3rd of 51 babylon escort Palm Bay functional household regarding CAZY databases, a glycosyl transferase class plan centered on catalytic residue and you can series homology considerations, might be unified from this prominent predict bend. 4% of the many non-redundant sequences and you can regarding the step one% off healthy protein in the Escherichia coli genome can be found in order to fall-in to your GPGTF superfamily. PDF