Crystal structure of formycin 5'-phosphate: an explanation for its tight binding to AMP nucleosidase.
Formycin 5'-monophosphate (FMP) is a strong competitive inhibitor of AMP nucleosidase with Km/Kis from 1200 to 2600 depending on the source of the enzyme. The crystal structure of FMP has been determined in order to understand the basis for its high affinity for AMP nucleosidases and other biological properties. The key structural features of FMP are (1) the base is the N(7)-H tautomer, (2) the N(3) of the base forms an intramolecular hydrogen bond to the phosphate oxygen O(1), (3) the glycosyl torsion angle is syn with O(4')-C(1') relative to C(9)-C(4) being -6.43 degrees, and (4) the furanose ring pucker is C(3')-endo, with a pseudorotation angle of 20.3 degrees. The major difference between the AMP and FMP structures is that the glycosyl torsion angles differ by 190 degrees. The computed conformational energy necessary to distort AMP so that it has the same glycosyl torsion angle as FMP is 4.6 kcal/mol. This corresponds to a 2100-fold difference in binding energy, in good agreement with the observed interaction between AMP nucleosidase and FMP.
Giranda
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Department of Biochemistry, Temple University School of Medicine, Philadelphia, Pennsylvania 19140.
Berman
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HM
Schramm
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VL
D000903:Antibiotics, Antineoplastic / Q000378:metabolism*; D003461:Crystallography; D005573:Formycins / Q000378:metabolism*; D008958:Models, Molecular; D008968:Molecular Conformation; D009699:N-Glycosyl Hydrolases / Q000378:metabolism*; D011485:Protein Binding; D012265:Ribonucleotides / Q000378:metabolism*; D014961:X-Ray Diffraction
D000903:Antibiotics, Antineoplastic; D005573:Formycins; D012265:Ribonucleotides; C021683:formycin 5'-phosphate; D009699:N-Glycosyl Hydrolases; C019699:AMP nucleosidase