Protein L-arabinose binding

F. A. Quicho and N. K. Vyas, Novel stereospecificity of the L-arabinose binding protein,... 

Fig. 21. Stereodrawing of L-arabinose bound to L-arabinose-binding protein from Escherichia coli. The edge-to-face interaction between tryptophan-16 and phenylalanine-17 gives rise to a hydrophobic surface that interacts with the hydrophobic portion of the sugar. Reproduced with permission from Quiocho and Vyas (1984).

Gilliland, G. L. and Quiocho, F. Q. (1981) Structure of the L-Arabinose-binding Protein From Escherichia coliat2.4 A Resolution,/. Mol. Biol. 146,341-362. 

Newcomer, M. E., Lewis, B. A. and Quiocho, F. A. (1981) The Radius of Gyration of L-Arabinose-binding Protein Decreases upon Binding of Ligand, J. Biol. Chem. 256, 13218-13222. 

Table 1 Correlations of binding affinity prediction for seven published knowledge-based scoring functions for the PMF validation sets of 77 protein-ligand complexes (all) which consist of five classes [47] 16 serine protease (Ser), 15 metalloprotease (Met), 18 L-arabinose binding protein (L-ara), 11 endothiapepsin (End), and 17 diverse protein-ligand complexes (Oth)... 

Figure 5. Extensive hydrogen-bonding interactions of Arg-151 of L-arabinose binding protein with L-arabinose. Three arrays of hydrogen bonds exist two neutral (to the backbone) and one ionic (to charged side chains) stabilize the buried Arg-151, including hydrogen bonding to the ring oxygens of the bound L-arabinose.

These principles are well illustrated by the 1.1-k analysis of the L-arabinose complex with L-arabinose-binding protein shown in Fig. 2 44). The extensively refined structure is the most detailed example of a hydrogen bond network at a... 

Fio. 2. Schematic representation from the extensively refined structure analysis of L-arabinose complexed with the L-arabinose-binding protein. Two levels of hydrogen bonds stabilizing the structure are shown. The residues in shell I hydrogen bond to L-arabinose and to shell II. Adapted horn Quiocho and Vyas (44) with permission from Nature. 

Fig. 1 Crystal structures of the periplasmic L-arabinose-binding protein (ABP) of Escherichia coli complexed to a-L-arabinose (left. PDB entry lABE) and of galectin-1 complexed to A-acetyllactosamine (right, PDB entry ISLT). (From Refs. [13-15]). (View this art in color at www.dekker.com.)...

The L-arabinose-binding protein from Escherichia coli also shows two domains with a cleft between them. Quiocho et in this case too, comment on the similarities between the secondary-structural features of these domains, each... 

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