Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP(+)

Structural data from two independent crystal forms (P2(1)2(1)2(1) and P2(1) ) of the folate (FA) binary complex and from the ternary complex with the o xidized coenzyme, NADP(+), and recombinant Pneumocystis carinii dihydrofola te reductase (pcDHFR) refined to an average of 2.15 Angstrom resolution, sh ow the first evidence of ligand-induced conformational changes in the struc ture of pcDHFR. These data are also compared with the crystal structure of the ternary complex of methotrexate (MTX) with NADPH and pcDHFR in the mono clinic lattice with data to 2.5 Angstrom resolution. Comparison of the data for the FA binary complex of pcDHFR with those for the ternary structures reveals significant differences, with a >7 Angstrom movement of the loop re gion near residue 23 that results in a new "flap-open" position for the bin ary complex, and a "closed" position in the ternary complexes, similar to t hat reported for Escherichia coli (ec) DHFR complexes. In the orthorhombic lattice for the binary FA pcDHFR complex, there is also an unwinding of a s hort helical region near residue 47 that places hydrophobic residues Phe-46 and Phe-49 toward the outer surface, a conformation that is stabilized by intermolecular packing contacts. The pyrophosphate moiety of NADP+ in the t ernary folate pcDHFR complexes shows significant differences in conformatio n compared with that observed in the MTX-NADPH-pcDHFR ternary complex. Addi tionally, comparison of the conformations among these four pcDHFR structure s reveals evidence for subdomain movement that correlates with cofactor bin ding states. The larger binding site access in the new "flap-open" loop 23 conformation of the binary FA complex is consistent with the rapid release of cofactor from the product complex during catalysis as well as the more r apid release of substrate product from the binary complex as a result of th e weaker contacts of the closed loop 23 conformation, compared to ecDHFR.