PDBsum entry: 1dc8

Signaling protein

PDB id: 1dc8

Contents

Protein chain

124 a.a. *

* Residue conservation analysis

PDB id:

1dc8

Name:

Signaling protein

Title:

Structure of a transiently phosphorylated "switch" in bacterial signal transduction

Structure:

Nitrogen regulation protein. Chain: a. Fragment: n-terminal receiver domain(1-124). Synonym: ntrc. Engineered: yes. Mutation: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

1 models

Authors:

D.Kern,B.F.Volkman,P.Luginbuhl,M.J.Nohaile,S.Kustu, D.E.Wemmer

Key ref:

D.Kern et al. (1999). Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature, 402, 894-898. PubMed id: 10622255 DOI: 10.1038/47273

Date:

04-Nov-99 Release date: 05-Jan-00

Protein chain

P41789  (NTRC_SALTY) -  Nitrogen regulation protein NR(I)

Seq: 469 a.a.

Struc: 124 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: two-component signal transduction system (phosphorelay) (2 terms)
• Biochemical function: two-component response regulator activity (1 term)

DOI no: 10.1038/47273

Nature 402:894-898 (1999)

PubMed id: 10622255

Structure of a transiently phosphorylated switch in bacterial signal transduction.

D.Kern, B.F.Volkman, P.Luginbühl, M.J.Nohaile, S.Kustu, D.E.Wemmer.

ABSTRACT

Receiver domains are the dominant molecular switches in bacterial signalling. Although several structures of non-phosphorylated receiver domains have been reported, a detailed structural understanding of the activation arising from phosphorylation has been impeded by the very short half-lives of the aspartylphosphate linkages. Here we present the first structure of a receiver domain in its active state, the phosphorylated receiver domain of the bacterial enhancer-binding protein NtrC (nitrogen regulatory protein C). Nuclear magnetic resonance spectra were taken during steady-state autophosphorylation/dephosphorylation, and three-dimensional spectra from multiple samples were combined. Phosphorylation induces a large conformational change involving a displacement of beta-strands 4 and 5 and alpha-helices 3 and 4 away from the active site, a register shift and an axial rotation in helix 4. This creates an exposed hydrophobic surface that is likely to transmit the signal to the transcriptional activation domain.

Selected figure(s)

Figure 2.
Figure 2: The structure of the phosphorylated receiver domain of NtrC. The 20 conformers with the lowest DYANA^28 target function were superimposed using the backbone atoms N, C and C' of residues 3–83 ( 1–loop 3), 87–96 ( 4) and 98–122 ( 5– 5), the best-defined areas (global backbone displacement <2.0 Å). Helices are coloured in yellow, strands in magenta and loops and chain termini in cyan. The side chain of the phosphorylated D54 is shown in green. The secondary structure elements are labelled as they are referred to in the text.

Figure 3.
Figure 3: Molecular switch upon phosphorylation of D54 in NtrC^r.
Figure 3 : Molecular switch upon phosphorylation of D54 in NtrCr. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
Superimposed ribbon structures of P-NtrC^r (yellow/orange) and NtrC^r (cyan/blue), generated using the conformer closest to the mean structure for each. The molecule has been rotated by 20° about the vertical axis with respect to Fig. 2 to emphasize the regions of structural differences between the two forms. Structures were superimposed using residues 4–9, 14–53 and 108–121, which are indicated in darker colours (orange and blue). The regions of greatest difference are highlighted (yellow and cyan, the switch area) and the corresponding secondary structure elements are labelled, with the prime indicating the unphosphorylated form. Upon phosphorylation of D54, -strands 4 and 5 and -helices 3 and 4 tilt to the left—away from the active site. In addition, a register shift by about two amino-acid residues from the N to the C terminus and a rotation by about 100° about the helical axis are induced in helix 4 upon phosphorylation. The rotation results in a change in orientation of the hydrophobic side chains in helix 4 from the inside to the outside.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 402, 894-898) copyright 1999.

Figures were selected by an automated process.