Determination of the nuclear magnetic resonance structure of the DNA-binding domain of the P22 c2 repressor (1 to 76) in solution and comparison with the DNA-binding domain of the 434 repressor.
The solution structure of the N-terminal DNA-binding domain of the P22 c2 repressor (residues 1 to 76) was determined by nuclear magnetic resonance (NMR) spectroscopy. The structure determination was based on nearly complete sequence-specific resonance assignments for 1H, 13C and 15N, and tables of the chemical shifts for all three nuclei are included here. A group of 20 conformers was calculated from the NMR constraints using the program DIANA, and energy-minimized using an implementation of the AMBER force field in the program OPAL. The core of the protein formed by residues 5 to 68 is structurally well defined, with an average of 0.7 A for the root-mean-square deviations calculated for the backbone atoms of the individual conformers relative to the mean coordinates. The N-terminal tetrapeptide segment and the C-terminal octapeptide segment are flexibly disordered. The molecular architecture includes five alpha-helical segments with residues 6 to 17, 21 to 28, 32 to 39, 47 to 57 and 61 to 65. The length and relative orientation of these helices are closely similar to the arrangement of corresponding regular secondary structures in the DNA-binding domain of the 434 repressor, with the sole exception of the fourth helix, which is one turn longer at its amino-terminal end than the corresponding helix in the 434 repressor. This extension of the fourth helix implies that the DNA-binding mode of the P22 c2 repressor must be somewhat different from that observed for the 434 repressor. Exact superposition of two P22 c2 repressor DNA-binding domains for best fit of corresponding polypeptide backbone atoms onto the two 434 repressor DNA-binding domains in the crystal structure of the 434 repressor-DNA complex would result in a model of the P22 c2 repressor-DNA complex which could not accommodate the fourth helices because of steric overlap.
Sevilla-Sierra
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Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
Otting
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G
Wüthrich
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D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D017100:Bacteriophage P22 / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins; D012097:Repressor Proteins / Q000737:chemistry*; D012996:Solutions; D012997:Solvents; D014764:Viral Proteins / Q000737:chemistry*; D054334:Viral Regulatory and Accessory Proteins
C063367:434-repressor protein, Bacteriophage 434; D000577:Amides; D004268:DNA-Binding Proteins; D011994:Recombinant Proteins; D012097:Repressor Proteins; D012996:Solutions; D012997:Solvents; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins