Sequence motif

The classic zinc fingers, the DNA-binding properties of which are discussed in Chapter 10, are small compact domains of about 30 residues that fold into an antiparallel p hairpin followed by an a helix. All known classic zinc fingers have a zinc atom bound to two cysteines in the hairpin and two histidines in the helix, creating a sequence motif common to all zinc finger genes. In the absence of zinc the structure is unfolded. 

The NBD unit harbors several conserved sequence motifs (Walker A and B, ABC-signature motifs), which... 

Nuclear factor kappa B (NF-kB) is the generic term for a family of dimeric eukaryotic transcription factors, composed of members of the Rel family of DNA-binding proteins including the mammalian proteins RelA (or p65), cRel, RelB, p50 and p52, and the Drosophila proteins Dorsal, Dif and Relish. These proteins bind with different affinities to a consensus DNA sequence motif (called the kB site) consisting of the sequence 5 -GGGRNNYYCC-3 in which R is a purine, Y is a pyrimidine, and N is any base. 

S6K1 (also known as p70S6 kinase) is a serine/ threonine protein kinase which is involved in the regulation of translation by phosphorylating the 40S ribosomal protein S6. Insulin and several growth factors activate the kinase by phosphorylation in a PI 3-kinase dependent and rapamycin-sensitive manner. Phosphorylation of S6 protein leads to the translation of mRNA with a characteristic 5 polypyrimidine sequence motif. 

Lohmann V, Komer F, Herian U, Bartenschlager R (1997) Biochemical properties of hepatitis C vims NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J Virol 71 8416-8428... 

In order to check whether the occurrence of the Rieske-type sequence motif is unique for the assimilatory nitrite reductase from Bacillus subtilis, the sequences of other assimilatory nitrite reductases were searched for the presence of the four putative ligands of Rieske-type clusters. A well-conserved sequence pattern... 

Cluster Fx was also identified via its EPR spectral features in the RCI photosystem from green sulfur bacteria 31, 32) and the cluster binding motif was subsequently found in the gene sequence 34 ) of the (single) subunit of the homodimeric reaction center core (for a review, see 54, 55)). Whereas the same sequence motif is present in the RCI from heliobacteria (50), no EPR evidence for the presence of an iron-sulfur cluster related to Fx has been obtained. There are, however, indications from time-resolved optical spectroscopy for the involvement of an Fx-type center in electron transfer through the heliobacterial RC 56). 

Resilin-like polypeptide and sequence motif Technique Helices (%) Strands (%) Turns (%) Unordered (%) (or random coil) Beta sheet (%) PPII (%)... 

Huttenrauch F, Nitzki A, Lin FT, Honing S, Oppermann M (2002) Beta-arrestin binding to CC chemokine receptor 5 requires multiple C-terminal receptor phosphorylation sites and involves a conserved Asp-Arg-Tyr sequence motif. J Biol Chem 277 30769-30777 Imitola J, Raddassi K, Park KI, Mueller FJ, Nieto M, Teng YD, Frenkel D, Li J, Sidman RL, Walsh CA, Snyder EY, Khoury SJ (2004) Directed migration of neural stem cells to sites of CNS injury by the stromal cell-derived factor lalpha/CXC chemokine receptor 4 pathway. Proc Natl Acad Sci U S A 101 18117-18122... 

The paired box is another sequence motif that is very well conserved during evolution and is found in a number of genes known to be of developmental significance in lower organisms. The paired box encodes the 128-amino acid paired domain, which binds DNA(Chalapakis et al., 1991), and shows similarity, with a helix-tum-helix motif, to the homeodomain. 

Cheng X, Collins RE, Zhang X (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annu Rev Biophys Biomolec Struct 34 267-294... 

Protein Source Diiron site function Diiron-binding sequence motif Diiron(III) solvent bridge... 

Sequence motifs in brackets are proposed others are based on X-ray crystal structures of the diiron-containing proteins. 6May not be a diiron-oxo protein as defined here. 

The gene encoding PBAN was first characterized from H. zea and B. mori [134,137,138,195]. The cDNA was found to encode the 33 amino acid PBAN plus four additional peptides with a common C-terminal FXPRL sequence motif, including that of the diapause hormone of B. mori (Fig. 6). Three additional peptides with the common C-termini and sequence homology to those of H. zea and B. mori have been deduced from cDNA isolated from pheromone glands of several other moths [194,196-200]. Studies conducted to find the post-translational processed peptides indicated that PBAN was found to a greater extent in the mandibular and maxillary clusters than in the labial cluster of neurons... 

Von Bergen, M. etal. Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif [306QIVYK311] forming beta structure. Proc. Natl. Acad. Sci. USA 97 5129-5134, 2000. 

Doubly-Lipid Modified Protein Sequence Motifs Exhibit Long-Lived Anchorage to Lipid Bilayer Membranes, S. Shahinian, J. R. Silvius, Biochemistry 1995, 34, 3813-3822. 

C. Recurring Conformations and Amino Acid Sequence Motifs of p-Arcs... 

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