1R62

Crystal structure of the C-terminal Domain of the Two-Component System Transmitter Protein NRII (NtrB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the C-terminal Domain of the Two-Component System Transmitter Protein Nitrogen Regulator II (NRII; NtrB), Regulator of Nitrogen Assimilation in Escherichia coli.

Song, Y.Peisach, D.Pioszak, A.A.Xu, Z.Ninfa, A.J.

(2004) Biochemistry 43: 6670-6678

  • DOI: https://doi.org/10.1021/bi049474r
  • Primary Citation of Related Structures:  
    1R62

  • PubMed Abstract: 

    The kinase/phosphatase nitrogen regulator II (NRII, NtrB) is a member of the transmitter protein family of conserved two-component signal transduction systems. The kinase activity of NRII brings about the phosphorylation of the transcription factor nitrogen regulator I (NRI, NtrC), causing the activation of Ntr gene transcription. The phosphatase activity of NRII results in the inactivation of NRI-P. The activities of NRII are regulated by the signal transduction protein encoded by glnB, PII protein, which upon binding to NRII inhibits the kinase and activates the phosphatase activity. The C-terminal ATP-binding domain of NRII is required for both the kinase and phosphatase activities and contains the PII binding site. Here, we present the crystal structure of the C-terminal domain of a mutant form of NRII, NRII-Y302N, at 1.6 A resolution and compare this structure to the analogous domains of other two-component system transmitter proteins. While the C-terminal domain of NRII shares the general tertiary structure seen in CheA, PhoQ, and EnvZ transmitter proteins, it contains a distinct beta-hairpin projection that is absent in these related proteins. This projection is near the site of a well-characterized mutation that reduces the binding of PII and near other less-characterized mutations that affect the phosphatase activity of NRII. Sequence alignment suggests that the beta-hairpin projection is present in NRII proteins from various organisms, and absent in other transmitter proteins from Escherichia coliK-12. This unique structural element in the NRII C-terminal domain may play a role in binding PII or in intramolecular signal transduction.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen regulation protein NR(II)160Escherichia coli K-12Mutation(s): 0 
Gene Names: NTRB
EC: 2.7.3 (PDB Primary Data), 2.7.13.3 (UniProt), 3.1.3 (UniProt)
UniProt
Find proteins for P0AFB5 (Escherichia coli (strain K12))
Explore P0AFB5 
Go to UniProtKB:  P0AFB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFB5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.44α = 90
b = 32.94β = 108.19
c = 46.01γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references