A/p proteins

EB Shemerman, CL Brooks III. Molecular picture of folding of a small a/p protein. Proc Natl Acad Sci USA 95 1562-1567, 1998. 

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

In this structure the loop regions adjacent to the switch point do not provide a binding crevice for the substrate but instead accommodate the active-site zinc atom. The essential point here is that this zinc atom and the active site are in the predicted position outside the switch point for the four central parallel p strands, even though these p strands are only a small part of the total structure. This sort of arrangement, in which an active site formed from parallel p strands is flanked by antiparallel p strands, has been found in a number of other a/p proteins with mixed p sheets. 

Janin, J., Chothia, C. Packing of a-helices onto p-pleat-ed sheets and the anatomy of a/p-proteins. /. Mol. Biol. 143 95-128, 1980. 

The active site of subtilisin is outside the carboxy ends of the central p strands analogous to the position of the binding sites in other a/p proteins as discussed in Chapter 4. Details of this active site are surprisingly similar to those of chymotrypsin, in spite of the completely different folds of the two enzymes (Figures 11.14 and 11.9). A catalytic triad is present that comprises residues Asp 32, His 64 and the reactive Ser 221. The negatively charged oxygen atom of the tetrahedral transition state binds in an oxyanion hole,... 

The 2.8 A resolution crystal structure of the arginase from the thermophilic bacterium Bacillus caldevelox [112] reveals a hexameric structure with at least one Mn2+ bound per subunit. The 2.1 A resolution structure of rat liver arginase, reported recently [81], reveals it to be trimeric, with the overall fold of the arginase monomer belonging to the a/p protein class. The Mn"Mnn aggregate, shown in Figure 24, is found at the bottom of a 15 A active-site cleft. 

Figure 2-27 Topologies of the folds of three families of nucleotide binding a/P proteins. Cylinders represent a helices and arrows P strands. (A) The ATPase fold for the clathrin-uncoating ATPase (B) The G-protein fold that binds GTP and is found in ras proteins (G) The Rossmann fold that binds NAD in several dehydrogenases. From Branden.2 =2...

Minton, A.P. Protein folding thickening the broth. Curr. Biol. 2000, 10, R97-R99. 

Figure 1. Some protein structures solved by X-ray crystallography. The figure illustrates the different secondary structure assemblies. a-Helices are represented by spirals or cylinders -strands by arrows, (a) Hemerythrin, an all a-protein. (b) Superoxide dismutase, an all /7-protein, (c) Lysozyme, an a -i- /7 protein, (d) and (e) Two orthogonal views of the NAD binding domain of lactate dehydrogenase, an a/p protein, (f) Triose phosphate isomerase, an a/p structure, (g) A DNA binding protein, the CAP protein from E. coli. (h) Influenza virus haemaglutinin. (i) Influenza virus neuraminidase. From Blake and Johnson [12b], which also contains references to the original sources of these structures.

Kinases FP, TR-FRET, IMAP, thermal melt Lysed—FRET, AlphaScreen , Alpha-LISA Intact— PathHunter kinase [47] Specific a-P-protein mAb staining fixed and permeabilized cells... 

The three-dimensional structure of bovine pancreatic DNase I was first determined at 2.5 A resolution by x-ray diffraction from single crystals [23]. DNase I proved to be a compact a,P-protein with two six-stranded j) sheets packed against each other forming the core of a sandwich -type structure. The two mainly antiparallel P sheets are flanked by three longer and five short a-helices and extensive loop regions (Fig. 3). 

Figure 1.29 Alternative cartoon depictions of proteins, (a) surface display structure of small metal rich protein cytochrome c (horse heart) (pdb Ihrc) showing Van der Waal s surface coloured for positive charge (blue) and for negative charge (red). Ball and stick representations of iron-porphyrin macrocycle (prosthetic group) are shown (red) for each subunit with central iron ion rendered as Van der Waals sphere (light blue) (b) CPK structure of cytochrome c in which all polypeptide atoms are rendered as Van der Waals spheres (purple). Porphryin and iron ion are shown as in Fig. 1.28 (c) schematic display structure (top view) of parallel a/p-protein triose phosphate isomerase (chicken muscle) (pdb Itim) with a-helix shown as cylinders (red), 8-strands as arrowed ribbons (light blue), loop structures (random coil) as rods (light grey) (d) schematic display structure (side view) of triose phosphate isomerase, otherwise as for (c).

Fig. 4-12 Stylized drawings of protein structures in which a helices are represented as coiled ribbons and p strands are represented by arrows pointing in the N -> C direction, (a) A p protein (b) a p protein (c) an a protein and (d) an a-P protein.

The motif Pap, which is prominent in the a/p proteins, is absent in protein a -i- p structures (e.g. lysozyme, papain) with separate a helices and P strands in different parts... 

Proteins built up entirely from a-helices include the globin and hanerythrin families and bacterioihodopsin. These are transport proteins and membrane-bound proteins. All-P proteins invariably consist of a sandwich of two layers, each a sheet held together by a hydrophobic core formed by one side from each sheet. Often the sheet is rounded to form a P-barrel. The P interactions in these proteins are usually antiparallel because there are no helices available to form the necessary crossover connections required for parallel P-sheets. The novel family of proteins with an all-parallel P-helix (Jumak et al, 1994 Yoder et al, 1993) is a remarkable exception. Proteins with distinct regions of all-a or all-P structures are called a + P proteins. The most complex class is the o/p proteins. In these, segments of a-helix and P-sheet follow one another, and consequently each of the two classes of secondary structure is intimately involved in stabilization of the other. For this reason, the P-structures are often parallel, since the presence of helices provides the necessary crossover connections. The -class of proteins is an ill-defined catchall (Chou, 1995). It includes a number of large peptides with no globular structure. 

Although no firm correlation can be established between the type of fold and the function of protein, there appears to be some correlation between the ligands bound and fold type. For example, NAD(P) /NAD(P)H cofactors show a preference for binding to o/p Ross-mann-like folds and DNA to mainly-a receptor-Uke folds. Furthermore, some functions are more frequently observed in particular stractural class. For example, enzymes are much more commonly a-p proteins, while extracellular proteins are frequently mainly-p. 

Linear or open P-a-P proteins. Many proteins that bind nucleotides... 

---