1NTC

SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF NTRC WITH THREE ALANINE SUBSTITUTIONS

Summary for 1NTC

• Entry DOI: 10.2210/pdb1ntc/pdb
• Descriptor: PROTEIN (NITROGEN REGULATION PROTEIN (NTRC)) (1 entity in total)
• Functional Keywords: helix-turn-helix, fis, four-helix bundle, transcription regulation
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 2
• Total formula weight: 19986.45

Authors

Pelton, J.G.,Kustu, S.,Wemmer, D.E. (deposition date: 1999-05-26, release date: 1999-06-04, Last modification date: 2023-12-27)

Primary citation

Pelton, J.G.,Kustu, S.,Wemmer, D.E.
Solution structure of the DNA-binding domain of NtrC with three alanine substitutions.
J.Mol.Biol., 292:1095-1110, 1999

PubMed Abstract: The structure of the 20 kDa C-terminal DNA-binding domain of NtrC from Salmonella typhimurium (residues Asp380-Glu469) with alanine replacing Arg456, Asn457, and Arg461, was determined by NMR spectroscopy. NtrC is a homodimeric enhancer-binding protein that activates the transcription of genes whose products are required for nitrogen metabolism. The 91-residue C-terminal domain contains the determinants necessary for dimerization and DNA-binding of the full length protein. The mutant protein does not bind to DNA but retains many characteristics of the wild-type protein, and the mutant domain expresses at high yield (20 mg/l) in minimal medium. Three-dimensional (1)H/(13)C/(15)N triple-resonance, (1)H-(13)C-(13)C-(1)H correlation and (15)N-separated nuclear Overhauser effect (NOE) spectroscopy experiments were used to make backbone and side-chain (1)H,(15)N, and (13)C assignments. The structures were calculated using a total of 1580 intra and inter-monomer distance and hydrogen bond restraints (88 hydrogen bonds; 44 hydrogen bond restraints), and 88 phi dihedral restraints for residues Asp400 through Glu469 in both monomers. A total of 54 ambiguous restraints (intra or inter-monomer) involving residues close to the 2-fold symmetry axis were also included. Each monomer consists of four helical segments. Helices A (Trp402-Leu414) and B (Leu421-His440) join with those of another monomer to form an antiparallel four-helix bundle. Helices C (Gln446-Leu451) and D (Ala456-Met468) of each monomer adopt a classic helix-turn-helix DNA-binding fold at either end of the protein. The backbone rms deviation for the 28 best of 40 starting structures is 0.6 (+/-0.2) A. Structural differences between the C-terminal domain of NtrC and the homologous Factor for Inversion Stimulation are discussed.

PubMed: 10512705
DOI: 10.1006/jmbi.1999.3140

Experimental method

SOLUTION NMR