Structural binding motifs

Kisselev, O. G., Kao, J., Ponder, J. W Fann, Y. C., Gautam, N. and Marshall, G. R. (1998) Light-activated rhodopsin induces structural binding motif in G protein a subunit. Proc. Natl. Acad. Sci. 95,4270 1275. 

Figure 1 Structural binding motifs for. (a)-(c) show the /3-strand motif, EF-hand motif, and helix turn motif, respectively, (d) shows a stereodiagram of the calcium binding domains in (a) and (b). (e) illustrates the ligand sites noted in the text. Backbone atoms are shown in yellow for (a) and green for (b) (reproduced with permission from Springer et al and Reid et al ).

Fricke H, Schafer G, Schrader T, Gerhards M (2007) Secondary structure binding motifs of the jet cooled tetrapeptide model Ac-Leu-Val-Tyr(Me)-NHMe. Phys Chem Chem Phys 9 4592... 

Simple combinations of a few secondary strucfure elements with a specific geometric arrangement have been found to occur frequently in protein structures. These units have been called either supersecondary structures or motifs. We will use the term "motif" throughout this book. Some of these motifs can be associated with a particular function such as DNA binding others have no specific biological function alone but are part of larger strucfural and functional assemblies. 

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. 

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. 

Fig. 6. A schematic view of the [3Fe-4S] Emd [4Fe-4S] cores, as versatile structures. The absence of one site leads to the formation of a [3Fe-4S] core. The cubane structure can incorporate different metals (in proteins, M = Fe, Co, Zn, Cd, Ni, Tl, Cs), and S, N, O may be coordinating atoms from hgands (Li). The versatihty csm be extended to higher coordination number at the iron site and a water molecule can even be a ligand, exchangeable with substrate (as in the case of aconitase (,87)). The most characteristic binding motifs are schematically indicated, for different situations proteins accommodating [3Fe-4S], [4Fe-4S], [3Fe-4S] + [4Fe-4S], and [4Fe-4S] -I- [4Fe-4S] clusters. A disulfide bridge may replace a cluster site (see text).

Tab. 3.1 DNA-binding proteins that have been inhibited by polyamides. The known DNA binding motifs from NMR or crystal structure data are shown. Significant groove contacts and proposed mechanism of polyamide inhibition are also shown for each protein...

These nuclear receptors have several common structural features (Figure 43-12). All have a centrally located DNA-binding domain (DBD) that allows the receptor to bind with high affinity to a response element. The DBD contains two zinc finger binding motifs (see Figure 39-14) that direct binding either as homodimers, as heterodimers (usually with a retinoid X... 

The biphenyl ligand functionalized with two imidazoles (6) was used to produce distorted tetrahedral complexes of zinc.119 2,2 -Biimidazole can act as a bidentate ligand coordinating to one zinc ion (7) or as a bridging ligand in the formation of dimeric species (8) with X-ray structures of both binding motifs.120... 

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