X-ray studies of nucleotide binding and pyridoxal phosphate labeling of the gene 5 DNA unwinding protein.
X-ray diffraction studies have been carried out using difference Fourier methods to evaluate the reaction or interaction of an affinity label and 5'-phosphate nucleotides with the gene 5 DNA binding protein in the crystalline state. In the first case the crystalline protein was reacted with pyridoxal phosphate. Pyridoxal phosphate, which has served as an affinity label for nucleotide binding sites on other enzymes, demonstrated a major site of substitution at the center of the protein's DNA binding cleft adjacent to lysine 46 as well as two other reaction sites near residues implicated in DNA binding. Difference Fourier maps of crystals exposed to 5'-dAMP, 5'-dCMP and 5'-dTMP indicated that phosphate groups were associated with most lysine and arginine side-chains on the surface of the protein but that the nucleoside portion of the ligands were generally disordered. In several cases, however, more specific binding of the nucleotides appeared to have occurred and these sites were primarily within the proposed DNA binding cleft of the protein. In particular, binding was observed near tyrosine 34, phenylalanine 73 and within the curl of the DNA binding loop containing tyrosine 26.
D000218:Adamantane / Q000031:analogs & derivatives / Q000378:metabolism; D000345:Affinity Labels / Q000378:metabolism; D001435:Bacteriophages; D001665:Binding Sites; D004265:DNA Helicases / Q000378:metabolism*; D003843:Deoxycytidine Monophosphate / Q000378:metabolism; D005583:Fourier Analysis; D008239:Lysine / Q000378:metabolism; D008958:Models, Molecular; D009711:Nucleotides / Q000378:metabolism*; D011732:Pyridoxal Phosphate / Q000378:metabolism*; D013938:Thymidine Monophosphate / Q000378:metabolism; D014961:X-Ray Diffraction
D000345:Affinity Labels; D009711:Nucleotides; D003843:Deoxycytidine Monophosphate; C016358:2,4-diamino-5-adamantyl-6-methylpyrimidine; D013938:Thymidine Monophosphate; D011732:Pyridoxal Phosphate; D004265:DNA Helicases; D008239:Lysine; D000218:Adamantane