2DTJ

Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum

Yoshida, A.Tomita, T.Kurihara, T.Fushinobu, S.Kuzuyama, T.Nishiyama, M.

(2007) J.Mol.Biol. 368: 521-536

  • DOI: 10.1016/j.jmb.2007.02.017
  • Also Cited By: 3AB4, 3AB2, 3AAW

  • PubMed Abstract: 
  • Aspartate kinase (AK) catalyzes the first step of the biosynthesis of the aspartic acid family amino acids, and is regulated via feedback inhibition by end-products including Thr and Lys. To elucidate the mechanism of this inhibition, we determined t ...

    Aspartate kinase (AK) catalyzes the first step of the biosynthesis of the aspartic acid family amino acids, and is regulated via feedback inhibition by end-products including Thr and Lys. To elucidate the mechanism of this inhibition, we determined the crystal structure of the regulatory subunit of AK from Corynebacterium glutamicum at 1.58 A resolution in the Thr-binding form, the first crystal structure of the regulatory subunit of alpha(2)beta(2)-type AK. The regulatory subunit contains two ACT domain motifs per monomer and is arranged as a dimer. Two non-equivalent ACT domains from different chains form an effector-binding unit that binds a single Thr molecule, and the resulting two effector-binding units of the dimer associate perpendicularly in a face-to-face manner. The regulatory subunit is a monomer in the absence of Thr but becomes a dimer by adding Thr. The dimerization is eliminated in mutant AKs with changes in the Thr-binding region, suggesting that the dimerization induced by Thr binding is a key step in the inhibitory mechanism of AK from C. glutamicum. A putative Lys-binding site and the inhibitory mechanism of CgAK are discussed.


    Related Citations: 
    • Conversion of feedback regulation in aspartate kinase by domain exchange
      Kato, C.,Kurihara, T.,Kobashi, N.,Yamane, H.,Nishiyama, M.
      (2004) Biochem.Biophys.Res.Commun. 316: 802
    • Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum
      Kalinowski, J.,Cremer, J.,Bachmann, B.,Eggeling, L.,Sahm, H.,Puhler, A.
      (1991) MOL.MICROBIOL. 5: 1197
    • Cloning of a DNA fragment from Corynebacterium glutamicum conferring aminoethyl cysteine resistance and feedback resistance to aspartokinase
      Thierbach, G.,Kalinowski, J.,Bachmann, B.,Puhler, A.
      (1990) APPL.MICROBIOL.BIOTECHNOL. 32: 443


    Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartokinase
A, B
178Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)Mutation(s): 0 
Gene Names: lysC
EC: 2.7.2.4
Find proteins for P26512 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  P26512
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
THR
Query on THR

Download SDF File 
Download CCD File 
A, B
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.989α = 90.00
b = 59.010β = 116.25
c = 75.782γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance