Structural superfamily

Staniforth, R. A., Giannini, S., Higgins, L. D., Conroy, M. J., Hounslow, A. M.,Jerala, R., Craven, C. J., and Waltho, J. P. (2001). Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. EMBO J. 20, 4774-4781. 

Stammers, D.K., Ren, J., Leslie, K. et al. 2001. The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehy-drogenase/reductases. Embo J 20 6619-6626. 

Staniforth RA, et al. Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. EMBO J. 2001 20 4774-4781. 

Figure 14. Zinc endoproteases a structural superfamily. The central panel shows the superposition of the alpha carbon atoms of the topologically equivalent catalytic domains of proteins from the long consensus family (silver) and the short spacer family (orange). Various consensus sequences are given (see text) with the zinc-chelating residues shown in white. Full blue arrows indicate presence of motif in observed three-dimensional structures corresponding to the zinc endoprotease fold shown in the central panel. Dotted lines indicate putative structure-sequence relationships discussed in the text.

McDonald, N.Q., Hendrickson, W.A., 1993. A new structural superfamily of growth factors defined by a cystine knot motif. Cell 73, 421-424. 

There is a second family of small lipid-binding proteins, the P2 family, which include among others cellular retinol- and fatty acid-binding proteins as well as a protein, P2, from myelin in the peripheral nervous system. However, members of this second family have ten antiparallel p strands in their barrels compared with the eight strands found in the barrels of the RBP superfamily. Members of the P2 family show no amino acid sequence homology to members of the RBP superfamily. Nevertheless, their three-dimensional structures have similar architecture and topology, being up-and-down P barrels. 

This is nicely illustrated by members of the chymotrypsin superfamily the enzymes chymotrypsin, trypsin, and elastase have very similar three-dimensional structures but different specificity. They preferentially cleave adjacent to bulky aromatic side chains, positively charged side chains, and small uncharged side chains, respectively. Three residues, numbers 189, 216, and 226, are responsible for these preferences (Figure 11.11). Residues 216... 

Conti, E., Franks, N. P., and Brick, P. (1996). Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 4 287-298. 

The extracellular domain of cadherins consists of a variable number of a repeated sequence of about 110 amino acids. This sequence is termed the cadherin repeat and resembles in overall structure, but not in sequence, the Ig like domains. The cadherin repeat is the characteristic motive common to all members of the cadherin superfamily. Classical and desmosomal cadherins contain five cadherin repeats, but as many as 34 repeats have been found in the FAT cadherin (see below). Cadherins are calcium-dependent cell adhesion molecules, which means that removal of Ca2+, e.g., by chelating agents such as EDTA, leads to loss of cadherin function. The Ca2+-binding pockets are made up of amino acids from two consecutive cadherin repeats, which form a characteristic tertiary structure to coordinate a single Ca2+ion [1]. 

Calpains. Figure 1 Domain structures of calpain superfamily. Figure kindly provided by Dr. Hiroyuki Sorimachi, Laboratory of Biological Function, University of Tokyo, Japan. 

Capsaicin, also known as N-Vanillyl-8-methyl-6-(E)-noneamide, is the most pungent of the group of compounds called capsaicinoids It is a common ingredient in varieties of pepper such as habanero, Thai, tabasco, cayenne etc. One target with which capsaicin interacts is the capsaicin receptor, an ion channel belonging to the superfamily of TRP channels. Because of the structural relation to other TRP channels and because the vanilloid moiety is an essential component of capsaicin, the capsaicin receptor is also called TRPVI or vanilloid receptor (VR1). It is involved in heat and pain perception. 

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