PDBsum entry: 1r63

Gene regulating protein

PDB id: 1r63

Contents

Protein chain

63 a.a. *

* Residue conservation analysis

PDB id:

1r63

Name:

Gene regulating protein

Title:

Structural role of a buried salt bridge in the 434 repressor DNA-binding domain, nmr, 20 structures

Structure:

Repressor protein from bacteriophage 434. Chain: a. Fragment: DNA-binding domain, residues 1 - 63. Engineered: yes

Source:

Phage 434. Organism_taxid: 10712. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

20 models

Authors:

K.V.Pervushin,M.Billeter,G.Siegal,K.Wuthrich

Key ref:

K.Pervushin et al. (1996). Structural role of a buried salt bridge in the 434 repressor DNA-binding domain. J Mol Biol, 264, 1002-1012. PubMed id: 9000626 DOI: 10.1006/jmbi.1996.0692

Date:

08-Nov-96 Release date: 16-Jun-97

Protein chain

P16117  (RPC1_BP434) -  Repressor protein CI (Fragment)

Seq: 95 a.a.

Struc: 63 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: DNA binding (2 terms)

DOI no: 10.1006/jmbi.1996.0692

J Mol Biol 264:1002-1012 (1996)

PubMed id: 9000626

Structural role of a buried salt bridge in the 434 repressor DNA-binding domain.

K.Pervushin, M.Billeter, G.Siegal, K.Wüthrich.

ABSTRACT

The independently folding 63-residue N-terminal DNA-binding domain of the 434 repressor, 434(1-63), contains a buried Arg10-Glu35 salt bridge. A corresponding salt bridge is found in a variety of prokaryotic and eukaryotic DNA-binding proteins with helix-turn-helix motifs. Here, the NMR solution structures of 434(1-63) and the mutant protein 434[R10M](1-63) were determined to investigate the structural role of this salt bridge. Both proteins contain the same type of global fold, with five alpha-helices and a helix-turn-helix motif formed by the helices II and III. The primary structural difference caused by the Arg10 --> Met mutation is a translation of helix I along its axis relative to the helix II-turn-helix III motif. This limited conformational change is paralleled by a 9 kJ M(-1) decrease of the stability of the folded mutant protein in aqueous solution at pH 4.8. It affects the pKa value of Glu19 as well as the population of a hydrogen bond between the backbone amide proton of Asn16 and the side-chain carboxylate group of Glu19. Using the crystal structure of the 434 repressor dimer complexed with the operator DNA as a basis, model building of the DNA complex with the NMR structure of 434[R10M](1-63) shows that Asn16, which is located on the protein surface, makes direct contact with the DNA and indicates that the point mutation Arg10 --> Met should also lead to modifications of the protein-protein contacts in the complex.

Selected figure(s)

Figure 1.
Figure 1. Plot of the number of NOE distance constraints per residue, n, versus the amino acid sequence of (a) 434(1--63) and (b) 434[R10M](1--63). The constraints are specified as follows: filled, intraresidual; cross- hatched, constraints between protons in sequentially neighboring residues; vertically hatched, constraints between protons located in residues separated by two to five positions along the sequence; open, all longer-range constraints.

Figure 8.
Figure 8. Model of a complex formed by a 434[R10M](1--63) dimer with an operator DNA. The view is along the axis of the recognition helix III in the major DNA groove for the cyan and yellow protein subunits. Parts of the crystal structure of the DNA complex with wild-type 434(1--69) (Aggarwal et al., 1988; PDB-entry 2OR1) are shown in green (DNA), yellow and pink (individual subunits of the 434 repressor dimer). Two molecules of 434[R10M](1--63) (cyan and violet) have been superimposed onto the corresponding segments of the individual 434(1--69) subunits in the crystal structure for optimal fit of the helix--turn--helix motif of residues 17 to 35. The side-chains of Ser55, Val56 and Asp57 are drawn in red and white, respectively, for the two 434[R10M](1--63) subunits. The broken lines connect residues in the two subunits that are at a short distance from each other.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 264, 1002-1012) copyright 1996.

Figures were selected by an automated process.