Refined solution structures of the Escherichia coli trp holo- and aporepressor.
The solution structures of the trp-repressor from Escherichia coli in both the liganded (holo-) and unliganded (apo-) form, have been refined by restrained molecular dynamics with simulated annealing using the program XPLOR and additional experimental constraints. The ensemble of refined holorepressor structures have a root-mean-square deviation (r.m.s.d.) of 0.8 A relative to the average structure for the backbone of the dimer core (helices A, B, C, A', B', C') and 2.5 A for the helix-turn-helix DNA-binding domain (helices D and E). The corresponding values for the aporepressor are 0.9 A for the backbone of the ABC-dimer core and 3.2 A for the DE helix-turn-helix. The r.m.s.d. of the average structures from the corresponding crystal structures are 2.3 A for the holorepressor ABC core and 4.2 A for its DE region; 2.3 A for the aporepressor core and 5.5 A for its DE region. The relative disorder of the DNA-binding domain is reflected in a number of experimental parameters including substantially more rapid backbone proton exchange rates, exchange-limited relaxation times and crystallographic B-factors. The stabilizing effect of the L-Trp ligand is evident in these measurements, as it is in the higher precision of the holorepressor structure.
Zhao
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Stanford Magnetic Resonance Laboratory, Stanford University, CA 94305-5055.
Arrowsmith
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Jia
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Jardetzky
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D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004926:Escherichia coli; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D012996:Solutions; D014364:Tryptophan; D029968:Escherichia coli Proteins
D001426:Bacterial Proteins; D012097:Repressor Proteins; D012996:Solutions; D014364:Tryptophan; C027190:TRPR protein, E coli; D029968:Escherichia coli Proteins