4USJ

N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom.

Chellamuthu, V.R.Ermilova, E.Lapina, T.Luddecke, J.Minaeva, E.Herrmann, C.Hartmann, M.D.Forchhammer, K.

(2014) Cell 159: 1188

  • DOI: 10.1016/j.cell.2014.10.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutamine is the primary metabolite of nitrogen assimilation from inorganic nitrogen sources in microorganisms and plants. The ability to monitor cellular nitrogen status is pivotal for maintaining metabolic homeostasis and sustaining growth. The pre ...

    Glutamine is the primary metabolite of nitrogen assimilation from inorganic nitrogen sources in microorganisms and plants. The ability to monitor cellular nitrogen status is pivotal for maintaining metabolic homeostasis and sustaining growth. The present study identifies a glutamine-sensing mechanism common in the entire plant kingdom except Brassicaceae. The plastid-localized PII signaling protein controls, in a glutamine-dependent manner, the key enzyme of the ornithine synthesis pathway, N-acetyl-l-glutamate kinase (NAGK), that leads to arginine and polyamine formation. Crystal structures reveal that the plant-specific C-terminal extension of PII, which we term the Q loop, forms a low-affinity glutamine-binding site. Glutamine binding alters PII conformation, promoting interaction and activation of NAGK. The binding motif is highly conserved in plants except Brassicaceae. A functional Q loop restores glutamine sensing in a recombinant Arabidopsis thaliana PII protein, demonstrating the modular concept of the glutamine-sensing mechanism adopted by PII proteins during the evolution of plant chloroplasts.


    Organizational Affiliation

    Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
A, B
318Arabidopsis thalianaMutation(s): 0 
Gene Names: NAGK
EC: 2.7.2.8
Find proteins for Q9SCL7 (Arabidopsis thaliana)
Go to Gene View: NAGK
Go to UniProtKB:  Q9SCL7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NITROGEN REGULATORY PROTEIN PII
C, D
154Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: GLB1
Find proteins for A8JI83 (Chlamydomonas reinhardtii)
Go to Gene View: GLB1
Go to UniProtKB:  A8JI83
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GLN
Query on GLN

Download SDF File 
Download CCD File 
C, D
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NLG
Query on NLG

Download SDF File 
Download CCD File 
A
N-ACETYL-L-GLUTAMATE
C7 H11 N O5
RFMMMVDNIPUKGG-YFKPBYRVSA-N
 Ligand Interaction
X2W
Query on X2W

Download SDF File 
Download CCD File 
B
N-ACETYL-L-GLUTAMYL 5-PHOSPHATE
N-ACETYL-5-OXO-5-(PHOSPHONOOXY)-L-NORVALINE
C7 H12 N O8 P
FCVIHFVSXHOPSW-YFKPBYRVSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A, B
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 171.430α = 90.00
b = 171.430β = 90.00
c = 171.430γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release