1J56

MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-Resolution Solution Structure of the Beryllofluoride-Activated NtrC Receiver Domain

Hastings, C.A.Lee, S.-Y.Cho, H.S.Yan, D.Kustu, S.Wemmer, D.E.

(2003) Biochemistry 42: 9081-9090

  • DOI: 10.1021/bi0273866
  • Primary Citation of Related Structures:  1KRW, 1KRX

  • PubMed Abstract: 
  • Bacterial receiver domains mediate the cellular response to environmental changes through conformational changes induced by phosphorylation of a conserved aspartate residue. While the structures of several activated receiver domains have recently bee ...

    Bacterial receiver domains mediate the cellular response to environmental changes through conformational changes induced by phosphorylation of a conserved aspartate residue. While the structures of several activated receiver domains have recently been determined, there is substantial variation in the conformational changes occurring upon activation. Here we present the high-resolution structure of the activated NtrC receiver domain (BeF(3)(-)-NtrC(r) complex) determined using NMR data, including residual dipolar couplings, yielding a family of structures with a backbone rmsd of 0.57 +/- 0.08 A, which is compared with the previous lower-resolution structure of the phosphorylated protein. Both phosphorylation and beryllofluoride addition induce a shift in register and an axial rotation of alpha-helix 4. In this high-resolution structure, we are able to observe a concerted change in the positions of Thr82 and Tyr101; this correlated change in two conserved residues (termed Y-T coupling) has been considered a general feature of the conformational change in receiver domains upon activation. In NtrC, this correlated side chain shift, leading to the helix reorientation, is distinctly different from the smaller reorganization seen in other activated receiver domains, and involves numerous other residues which do not participate in conformational changes seen in the other systems. Titration of the activated receiver domain with peptides from the NtrC ATPase domain provides direct evidence for interactions on the rearranged face of the receiver domain, which are likely to be responsible for enabling assembly into the active aggregate. Analysis of the active structure also suggests that His84 may play a role in controlling the phosphate hydrolysis rate.


    Related Citations: 
    • CRYSTAL STRUCTURE OF AN ACTIVATED RESPONSE REGULATOR BOUND TO ITS TARGET
      Lee, S.-Y.,Cho, H.S.,Pelton, J.G.,Yan, D.,Henderson, R.K.,King, D.S.,Huang, L.,Kustu, S.,Berry, E.A.,Wemmer, D.E.
      (2001) Nat.Struct.Mol.Biol. 8: 52
    • NMR STRUCTURE OF ACTIVATED CHEY
      Cho, H.S.,Lee, S.-Y.,Yan, D.,Pan, X.,Parkinson, J.S.,Kustu, S.,Wemmer, D.E.,Pelton, J.G.
      (2000) J.Mol.Biol. 297: 543


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROGEN REGULATION PROTEIN NR(I)
A
124Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: glnG (ntrC)
Find proteins for P41789 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P41789
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance