2XKO

Crystal structure of the complex of NtcA with its transcriptional co- activator PipX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Regulation of Ntca-Dependent Transcription by Proteins Pipx and Pii.

Llacer, J.L.Espinosa, J.Castells, M.A.Contreras, A.Forchhammer, K.Rubio, V.

(2010) Proc.Natl.Acad.Sci.USA 107: 15397

  • DOI: 10.1073/pnas.1007015107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PII, an ancient and widespread signaling protein, transduces nitrogen/carbon/energy abundance signals through interactions with target proteins. We clarify structurally how PII regulates gene expression mediated by the transcription factor NtcA, the ...

    PII, an ancient and widespread signaling protein, transduces nitrogen/carbon/energy abundance signals through interactions with target proteins. We clarify structurally how PII regulates gene expression mediated by the transcription factor NtcA, the global nitrogen regulator of cyanobacteria, shedding light on NtcA structure and function and on how NtcA is activated by 2-oxoglutarate (2OG) and coactivated by the nonenzymatic PII target, protein PipX. We determine for the cyanobacteria Synechococcus elongatus the crystal structures of the PII-PipX and PipX-NtcA complexes and of NtcA in active and inactive conformations (respective resolutions, 3.2, 2.25, 2.3, and 3.05 A). The structures and the conclusions derived from them are consistent with the results of present and prior site-directed mutagenesis and functional studies. A tudor-like domain (TLD) makes up most of the PipX structure and mediates virtually all the contacts of PipX with PII and NtcA. In the PII-PipX complex, one PII trimer sequesters the TLDs of three PipX molecules between its body and its extended T loops, preventing PipX activation of NtcA. Changes in T loop conformation triggered by 2OG explain PII-PipX dissociation when 2OG is bound. The structure of active dimeric NtcA closely resembles that of the active cAMP receptor protein (CRP). This strongly suggests that with these proteins DNA binding, transcription activation, and allosteric regulation occur by common mechanisms, although the effectors are different. The PipX-NtcA complex consists of one active NtcA dimer and two PipX monomers. PipX coactivates NtcA by stabilizing its active conformation and by possibly helping recruit RNA polymerase but not by providing extra DNA contacts.


    Organizational Affiliation

    Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas, Centro de Investigación Biomédica en Red de Enfermedades Raras, Jaime Roig 11, Valencia 46010, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLOBAL NITROGEN REGULATOR
A, B
222Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: ntcA
Find proteins for P29283 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  P29283
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PIPX
C, D
89Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Find proteins for Q7X386 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q7X386
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 52.020α = 90.00
b = 52.020β = 90.00
c = 227.730γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance