THE 1.6 ANGSTROM CRYSTAL-STRUCTURE OF THE ARAC SUGAR-BINDING AND DIMERIZATION DOMAIN COMPLEXED WITH D-FUCOSE

The crystal structure of the sugar-binding and dimerization domain of the Escherichia coli gene regulatory protein, AraC, has been determine d in complex with the competitive inhibitor D-fucose at pH 5.5 to a re solution of 1.6 Angstrom. An in-depth analysis shows that the structur al basis for AraC carbohydrate specificity arises from the precise arr angement of hydrogen bond-forming protein side-chains around the bound sugar molecule. van der Waals interactions also contribute to the epi meric and anomeric selectivity of the protein. The methyl group of D-f ucose is accommodated by small side-chain movements in the sugar-bindi ng site that result in a slight distortion in the positioning of the a mino-terminal arm. A comparison of this structure with the 1.5 Angstro m structure of AraC complexed with L-arabinose at neutral pH surprisin gly revealed very small structural changes between the two complexes. Based on solution data, we suspect that the low pH used to crystallize the fucose complex affected the structure, and speculate about the na ture of the changes between pH 5.5 and neutral pH and their implicatio ns for gene regulation by AraC. a comparison with the structurally unr elated E. coli periplasmic sugar-binding proteins reveals that conserv ed features of carbohydrate recognition are present, despite a complet e lack of structural similarity between the two classes of proteins, s uggesting convergent evolution of carbohydrate binding. (C) 1997 Acade mic Press Limited.