Nucleotide conserved motif

The Ras superfamily of GTP-binding proteins is composed of several subfamilies [7] which all contain the Ras-like domain of approximately 160 amino acids and 5 consensus sequences. Two of these highly conserved motifs are responsible for specific recognition of the guanosine nucleotide, and three are necessary for binding of the phosphate groups and complexation of a Mg++ ion, which is found in all Ras-like proteins. 

Fig. 10.3 Frequency of nucleotide occurrence within the two key motifs of the C glutamicum housekeeping promoters. The distribution is based on the alignment of 159 promoter sequences and represents the levels of nucleotide conservation in particular positions in -35 and -10 regions. The key -10 hexamer is underlined...

The ABC transporters are products of one of the largest gene superfamilies. Each consists of two cytoplasmic nucleotide-binding domains (NBDs) and two transmembrane domains (TMDs). The NBDs are highly conserved across the ABC family and contain motifs typical of ATP-binding sites, whereas the TMD structures vary, probably because they are adapted to the wide variety of substrates. In eukaryotes the C-terminal of each NBD is linked to a TMD. In some cases the functional unit is (NBD-TMD)2 and, in others, the first TMD is covalently linked to the second NBD. 

G-CSF expression is controlled at both the transcriptional and posttranscrip-tional levels. A sequence of 300 nucleotides upstream of the initiation codon is conserved in both the murine and human genes, and this appears to contain three regulatory sites. G-CSF (and some other cytokine genes) may be constitutively transcribed by cells such as blood monocytes, fibroblasts and endothelial cells, but the mRNA may be short-lived (fi/2 < 15 min). The mRNA contains poly-AUUUA sequences in the untranslated region, and this motif is usually associated with mRNA instability. Indeed, such regions have also been identified in mRNA for GM-CSF, IL-1, IL-6, interferons, TNF, some growth factors, c-jun, c-fos, c-myc and c-myb. Upon the addi-... 

Surprisingly, AGS 1 is a Ras-related protein with all the conserved Ras-like motifs required for nucleotide binding/hydrolysis and membrane localization (Fig. 4). AGSl also contains unique N- and C-terminal extensions not seen in the majority of Ras family members, as well as a short internal insert region (Fig. 4). Each of these extensions in AGS 1 con-... 

First identified in 1986 as the catalytic active element in the replication cycle of certain viruses, the hammerhead ribozymes (HHRz) are the smallest known, naturally occurring RNA endonucleases They consist of a single RNA motif which catalyzes a reversible, site-specific cleavage of one of its own phosphodiester bonds . Truncation of this motif allowed a minimal HHRz to be constructed which was the very first ribozyme to be crystallized. HHRz minimal motifs are characterized by a core of eleven conserved nucleotides (bold font in Figure 20) from which three helices of variable length radiate. Selective mutation of any of these conserved residues results in a substantial loss of activity. In the absence of metal ions the structure is relaxed ( extended ), but upon addition of Mg +, hammerhead ribozymes spontaneously fold into a Y-shaped conformation (Figure 20 Color Plate 3). ... 

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