Binding motifs

NifA proteins are of one of two types. One group consists of 02-sensitive NifA proteins, which are found in the rhizobia Bhodobacter and Ae spirillum. These proteins have a proposed iron-binding motif on a linker between the central and C-terminal domains that may form a redox-sensitive... 

One of these motifs, called the helix-turn-helix motif, is specific for DNA binding and is described in detail in Chapters 8 and 9. The second motif is specific for calcium binding and is present in parvalbumin, calmodulin, tro-ponin-C, and other proteins that bind calcium and thereby regulate cellular activities. This calcium-binding motif was first found in 1973 by Robert Kretsinger, University of Virginia, when he determined the structure of parvalbumin to 1.8 A resolution. 

Figure 2.12 Two a helices that are connected by a short loop region in a specific geometric arrangement constitute a helix-turn-helix motif. Two such motifs are shown the DNA-binding motif (a), which is further discussed in Chapter 8, and the calcium-binding motif (b), which is present in many proteins whose function is regulated by calcium.

Both lambda Cro and repressor proteins have a specific DNA-binding motif... 

The specific arrangement of two a helices joined by a loop region in lambda Cro and repressor, as well as in CAP, constitute the helix-turn-helix DNA-binding motif (Figure 8.8), which also occurs in some eucaryotic transcription factors as discussed in Chapter 9. The orientation of the two helices and... 

Brennan, R.G., Matthews, B.W. The helix-turn-helix DNA-binding motif. /. Biol. Chem. 264 1903-1906, 1989. 

The DNA-binding motifs discussed in this and the preceding two chapters are those most frequently found in procaryotes and eucaryotes. However, other motifs are known, for example the p sheet motif of the met repressor in Escherichia coli which binds to the major groove of DNA. No doubt others remain to be discovered. 

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

HBV, hepatitis B HCV, hepatitis C IAP, inhibitor of apoptosis protein DBM, IAP binding motifs INCA, inhibitory CARD NASH, non-alcoholic steatohepatitis PCD, programmed cell death PCI, pan-caspase inhibitor OA, osteoarthritis RA, rheumatoid arthritis Smac, second mitochondria-derived activator of caspases TRAIL, tumor necrosis factor-related apoptosis-inducing ligand. 

The ED5o is the dose of a drag required to achieve a half-maximal effect. A Ca2+-binding motif found in many Ca2+-binding proteins. 

A helix-loop-helix motif is a DNA-binding motif, related to the leucine-zipper. A helix-loop-helix motif consists of a short a helix, connected by a loop to a second, longer a helix. The loop is flexible and allows one helix to fold back and pack against the other. The helix-loop-helix structure binds not only DNA but also the helix-loop-helix motif of a second helix-loop-helix protein forming either a homodimer or a heterodimer. 

Formation of a novel binding site novel complexes may be formed between a SUMOylated protein and an effector protein that contains a SUMO-interacting motif (SIM or SBM). Proteins that contain two binding sites, a SIM and a weak binding motif to protein X, will bind more strongly to this protein if it is SUMOylated (Fig. 3b). Short peptides that contain the hydrophobic core motif [V/I]-X-[V/I]-[V/I] or [V/I-[V/I]]-X-[V/I] can act as a SIM and bind to SUMO. This core is often flanked by acidic amino acids and/or serine residues. 

TH Tec homology domain SH3-binding prolin-rich sequences and Znz+-binding motif... 

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