6MR9
E. coli DHFR complex with a reaction intermediate
Summary for 6MR9
| Entry DOI | 10.2210/pdb6mr9/pdb |
| Related | 6CW7 6CXK |
| Descriptor | Dihydrofolate reductase, CHLORIDE ION, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | dhfr, dihydrofolate reductase, tetrahydrofolate, complex, reaction intermediate, oxidoreductase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 19497.23 |
| Authors | Cao, H.,Rodrigues, J.,Benach, J.,Frommelt, A.,Morisco, L.,Koss, J.,Shakhnovich, E.,Skolnick, J. (deposition date: 2018-10-12, release date: 2019-05-15, Last modification date: 2023-10-11) |
| Primary citation | Cao, H.,Skolnick, J. Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate. Struct Dyn., 6:024701-024701, 2019 Cited by PubMed Abstract: Time-resolved crystallography is a powerful technique to elucidate molecular mechanisms at both spatial (angstroms) and temporal (picoseconds to seconds) resolutions. We recently discovered an unusually slow reaction at room temperature that occurs on the order of days: the reverse oxidative decay of the chemically labile (6S)-5,6,7,8-tetrahydrofolate in complex with its producing enzyme dihydrofolate reductase. Here, we report the critical analysis of a representative dataset at an intermediate reaction time point. A quinonoid-like intermediate state lying between tetrahydrofolate and dihydrofolate features a near coplanar geometry of the bicyclic pterin moiety, and a tetrahedral C6 geometry is proposed based on the apparent mFo-DFc omit electron densities of the ligand. The presence of this intermediate is strongly supported by Bayesian difference refinement. Isomorphous Fo-Fo difference map and multi-state refinement analyses suggest the presence of end-state ligand populations as well, although the putative intermediate state is likely the most populated. A similar quinonoid intermediate previously proposed to transiently exist during the oxidation of tetrahydrofolate was confirmed by polarography and UV-vis spectroscopy to be relatively stable in the oxidation of its close analog tetrahydropterin. We postulate that the constraints on the ligand imposed by the interactions with the protein environment might be the origin of the slow reaction observed by time-resolved crystallography. PubMed: 30868089DOI: 10.1063/1.5086436 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.35 Å) |
Structure validation
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