1skp
From Proteopedia
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NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES
Overview
The three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC), from the, promoter region of a gene regulating sporulation in Bacillus subtilis, mother cells, was determined utilizing two-dimensional nuclear Overhauser, effect (2D NOE) and double-quantum-filtered COSY (2QF-COSY) spectra. To, minimize the effect of methods used to obtain restraints and refine, structure, several variables were studied. Interproton distance bounds, were calculated very conservatively by running the complete relaxation, matrix program MARDIGRAS hundreds of times using 2D NOE spectra for, exchangeable and for nonexchangeable protons at different mixing times, assuming different overall correlation times and different starting, structures. The 435 distance restraints were used with two different, structural refinement methods: restrained molecular dynamics (rMD) and, restrained Monte Carlo calculations (rMC). Refinement using different, procedures and starting structures resulted in essentially the same, structure (<0.8 A rmsd), indicating that the structure is defined by, experimental restraints and not the refinement method or variables used. R, factors indicate the structures fit the experimental NOE data very well., Some helical parameters, notably large negative X displacement, are, characteristic of A-DNA, but others are characteristic of B-DNA. As with, TG.CA steps in other duplex DNA sequences studied in our laboratory, the, two TG.CA steps have a positive roll, with T6-G7 exhibiting the largest, and consequently a bent helix axis. The converged structure represents a, time-averaged structure. However, multiple conformations, especially in, deoxyriboses, were evident from vicinal coupling constants obtained from, quantitative simulations of 2QF-COSY cross-peaks and from persistent, inconsistencies in experimental distances due to nonlinear conformational, averaging.
About this Structure
1SKP is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase., Tonelli M, Ragg E, Bianucci AM, Lesiak K, James TL, Biochemistry. 1998 Aug 25;37(34):11745-61. PMID:9718297
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