2XBP

A novel signal transduction protein PII variant from Synechococcus elongatus PCC7942 indicates a two-step process for NAGK PII complex formation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

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Ligand Structure Quality Assessment 


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Literature

A Novel Signal Transduction Protein P(II) Variant from Synechococcus Elongatus Pcc 7942 Indicates a Two-Step Process for Nagk- P(II) Complex Formation.

Fokina, O.Chellamuthu, V.R.Zeth, K.Forchhammer, K.

(2010) J Mol Biol 399: 410

  • DOI: 10.1016/j.jmb.2010.04.018
  • Primary Citation of Related Structures:  
    2XBP

  • PubMed Abstract: 
  • P(II) signal transduction proteins are highly conserved in bacteria, archaea and plants and have key functions in coordination of central metabolism by integrating signals from the carbon, nitrogen and energy status of the cell. In the cyanobacterium Synechococcus elongatus PCC 7942, P(II) binds ATP and 2-oxoglutarate (2-OG) in a synergistic manner, with the ATP binding sites also accepting ADP ...

    P(II) signal transduction proteins are highly conserved in bacteria, archaea and plants and have key functions in coordination of central metabolism by integrating signals from the carbon, nitrogen and energy status of the cell. In the cyanobacterium Synechococcus elongatus PCC 7942, P(II) binds ATP and 2-oxoglutarate (2-OG) in a synergistic manner, with the ATP binding sites also accepting ADP. Depending on its effector molecule binding status, P(II) (from this cyanobacterium and other oxygenic phototrophs) complexes and regulates the arginine-controlled enzyme of the cyclic ornithine pathway, N-acetyl-l-glutamate kinase (NAGK), to control arginine biosynthesis. To gain deeper insights into the process of P(II) binding to NAGK, we searched for P(II) variants with altered binding characteristics and found P(II) variants I86N and I86T to be able to bind to an NAGK variant (R233A) that was previously shown to be unable to bind wild-type P(II) protein. Analysis of interactions between these P(II) variants and wild-type NAGK as well as with the NAGK R233A variant suggested that the P(II) I86N variant was a superactive NAGK binder. To reveal the structural basis of this property, we solved the crystal structure of the P(II) I86N variant at atomic resolution. The large T-loop, which prevails in most receptor interactions of P(II) proteins, is present in a tightly bended conformation that mimics the T-loop of S. elongatus P(II) after having latched onto NAGK. Moreover, both P(II) I86 variants display a specific defect in 2-OG binding, implying a role of residue I86 in 2-OG binding. We propose a two-step model for the mechanism of P(II)-NAGK complex formation: in an initiating step, a contact between R233 of NAGK and E85 of P(II) initiates the bending of the extended T-loop of P(II), followed by a second step, where a bended T-loop deeply inserts into the NAGK clefts to form the tight complex.


    Organizational Affiliation

    Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITROGEN REGULATORY PROTEIN P-IIA113Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 1 
Gene Names: glnBSynpcc7942_0321
UniProt
Find proteins for P0A3F4 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore P0A3F4 
Go to UniProtKB:  P0A3F4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP PDBBind:  2XBP Kd: 9600 (nM) from 1 assay(s)
Binding MOAD:  2XBP Kd: 9600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.682α = 90
b = 80.682β = 90
c = 80.682γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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