Sequence conserved elements

Bacterial promoters are approximately 40 nucleotides (40 bp or four turns of the DNA double helix) in length, a region small enough to be covered by an E coli RNA holopolymerase molecule. In this consensus promoter region are two short, conserved sequence elements. Approximately 35 bp upstream of the transcrip-... 

The structure of the mSos protein (m=mammalian) is shown in Fig. 9.8. Sequence comparison with known Ras-specific GEFs has identified a common domain of ca.200 amino acids, to which nucleotide exchange activity has been assigned. Within this domain, three highly conserved sequence elements can be differentiated, separated by more variable sections. Other structural elements include a PH domain and a Pro-rich binding domain. The Pro-rich sequence fimctions as an attachment site for the SH3 group of Grb2 protein. 

It is assumed that the Jak kinases bind to a cytoplasmic section of the receptor, which is in the vicinity of the membrane and contains two conserved sequence elements, Box 1 and Box 2. Binding of the Jak kinases leads to their activation, a process linked to mutual phosphorylation of the Jak kinases (Fig. 11.6). Activation of the Jak kinases may take place in a homodimeric receptor complex or it may also occm in hetero-oligomeric complexes. The circumstances are comphcated in that two (or more) Jak kinases may associate at an activated receptor. Two different Jak kinases are required for signal transduction via interferon receptors (see Fig. 11.8). Furthermore, the different Jak kinases are specific for the corresponding receptors. 

Falkner, F.G., Zachau, H.G. (1984). Correct transcription of an immunoglobulin K gene requires an upstream fragment containing conserved sequence elements. Nature 310,71-74. 

Once the set of superfamily members has been confirmed, the next step is to identify conserved sequence elements that can be associated with conserved functional steps among the member proteins. This will be most easily achieved for superfamilies in which one or more members have been mechanistically characterized and residues or motifs playing important chemical roles already identified. Here, inference based on analogy can be highly useful in predicting properties of uncharacterized proteins. This, generally, is one of the most common procedures in... 

Pre-mRNAs Contain Conserved Sequence Elements at the Splice Sites... 

RNA Polymerase II. Promoters for RNA polymerase 0, like prokaryotic promoters, include a set of conserved-sequence elements that define the start site and recruit the polymerase. However, the promoter can contain any combination of a number of possible elements. Unique to eukaryotes, tliey also include enhancer elements that can be very distant (more than 1 kb) from the start site (p. 838). 

Forkhead-associated domains (FHA domains) were originally identified as conserved sequence elements within a subset of forkhead transcription factors and were subsequently found, e. g., in other transcription factors, in protein kinases, protein phosphatases, and kinesin motors (review Durocher and Jackson, 2002). FHA domains comprise up to 140 amino acids, exhibit binding specificity toward phosphothreonine residues, and efficiently discriminate against phosphoserine residues. 

---