The structure of a yeast hexokinase monomer and its complexes with substrates at 2.7-A resolution

From a 2.7-A resolution electron density map we have built a model of the polypeptide backbone of a monomer of yeast hexokinase B (EC 2.7.1.1). This map was obtained from a third crystal form of hexokinase, called BIII, which exhibits space group P212121 and which contains only one monomer per asymmetric unit. The 51,000 molecular weight monomer has an elongated shape (80 A by 55 A by 50 A) and is divided into two lobes by a deep central cleft. The polypeptide chain is folded into three structural domains, one of which is predominantly alpha-helical and two of which each contain a beta-pleated sheet flanked by alpha-helices. Both glucose and AMP bind to these crystals and produce significant alterations in the protein structure. Glucose binds in the deep cleft, as was observed previously in the BII crystal of the dimeric enzyme. AMP, however, binds to a site that is different from the major intersubunit ATP binding site observed in the crystalline dimer. The AMP is found near one of the beta-pleated sheets. From our current interpretation of this electron density map we conclude that neither of the two nucleotide binding regions has the same structure as has been observed for the nucleotide binding regions of the dehydrogenases, adenylate kinase, and phosphoglycerate kinase, although some similarities exist.