2RD5

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Regulation of N-Acetylglutamate Kinase by PII in Arabidopsis thaliana.

Mizuno, Y.Moorhead, G.B.Ng, K.K.

(2007) J.Biol.Chem. 282: 35733-35740

  • DOI: 10.1074/jbc.M707127200

  • PubMed Abstract: 
  • PII is a highly conserved regulatory protein found in organisms across the three domains of life. In cyanobacteria and plants, PII relieves the feedback inhibition of the rate-limiting step in arginine biosynthesis catalyzed by N-acetylglutamate kina ...

    PII is a highly conserved regulatory protein found in organisms across the three domains of life. In cyanobacteria and plants, PII relieves the feedback inhibition of the rate-limiting step in arginine biosynthesis catalyzed by N-acetylglutamate kinase (NAGK). To understand the molecular structural basis of enzyme regulation by PII, we have determined a 2.5-A resolution crystal structure of a complex formed between two homotrimers of PII and a single hexamer of NAGK from Arabidopsis thaliana bound to the metabolites N-acetylglutamate, ADP, ATP, and arginine. In PII, the T-loop and Trp(22) at the start of the alpha1-helix, which are both adjacent to the ATP-binding site of PII, contact two beta-strands as well as the ends of two central helices (alphaE and alphaG) in NAGK, the opposing ends of which form major portions of the ATP and N-acetylglutamate substrate-binding sites. The binding of Mg(2+).ATP to PII stabilizes a conformation of the T-loop that favors interactions with both open and closed conformations of NAGK. Interactions between PII and NAGK appear to limit the degree of opening and closing of the active-site cleft in opposition to a domain-separating inhibitory effect exerted by arginine, thus explaining the stimulatory effect of PII on the kinetics of arginine-inhibited NAGK.


    Organizational Affiliation

    Department of Biological Sciences and the Alberta Ingenuity Centre for Carbohydrate Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylglutamate kinase-like protein
A, B
298Arabidopsis 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
PII protein
C, D
135Arabidopsis thalianaMutation(s): 0 
Gene Names: GLB1 (GLNB1)
Find proteins for Q9ZST4 (Arabidopsis thaliana)
Go to Gene View: GLB1
Go to UniProtKB:  Q9ZST4
Small Molecules
Ligands 5 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, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
A, B
N-ACETYL-L-GLUTAMATE
C7 H11 N O5
RFMMMVDNIPUKGG-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: 2.51 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 171.133α = 90.00
b = 171.133β = 90.00
c = 171.133γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
MxDCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description