3AB4

Crystal structure of feedback inhibition resistant mutant of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum

Yoshida, A.Tomita, T.Kuzuyama, T.Nishiyama, M.

(2010) J Biol Chem 285: 27477-27486

  • DOI: 10.1074/jbc.M110.111153
  • Primary Citation of Related Structures:  
    3AB2, 3AB4, 3AAW

  • PubMed Abstract: 
  • Aspartate kinase (AK) is the first and committed enzyme of the biosynthetic pathway producing aspartate family amino acids, lysine, threonine, and methionine. AK from Corynebacterium glutamicum (CgAK), a bacterium used for industrial fermentation of amino acids, including glutamate and lysine, is inhibited by lysine and threonine in a concerted manner ...

    Aspartate kinase (AK) is the first and committed enzyme of the biosynthetic pathway producing aspartate family amino acids, lysine, threonine, and methionine. AK from Corynebacterium glutamicum (CgAK), a bacterium used for industrial fermentation of amino acids, including glutamate and lysine, is inhibited by lysine and threonine in a concerted manner. To elucidate the mechanism of this unique regulation in CgAK, we determined the crystal structures in several forms: an inhibitory form complexed with both lysine and threonine, an active form complexed with only threonine, and a feedback inhibition-resistant mutant (S301F) complexed with both lysine and threonine. CgAK has a characteristic alpha(2)beta(2)-type heterotetrameric structure made up of two alpha subunits and two beta subunits. Comparison of the crystal structures between inhibitory and active forms revealed that binding inhibitors causes a conformational change to a closed inhibitory form, and the interaction between the catalytic domain in the alpha subunit and beta subunit (regulatory subunit) is a key event for stabilizing the inhibitory form. This study shows not only the first crystal structures of alpha(2)beta(2)-type AK but also the mechanism of concerted inhibition in CgAK.


    Related Citations: 
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AspartokinaseA, C, E, G, I, K, M, O421Corynebacterium glutamicumMutation(s): 0 
Gene Names: lysC
EC: 2.7.2.4
Find proteins for P26512 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P26512 
Go to UniProtKB:  P26512
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AspartokinaseB, D, F, H, J, L, N, P178Corynebacterium glutamicumMutation(s): 0 
Gene Names: lysC
EC: 2.7.2.4
Find proteins for P26512 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P26512 
Go to UniProtKB:  P26512
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
AA [auth G], FA [auth K], IA [auth M], LA [auth O], R [auth A], U [auth C], X [auth E]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
THR
Query on THR

Download Ideal Coordinates CCD File 
BA [auth H] , CA [auth I] , DA [auth J] , EA [auth K] , GA [auth L] , HA [auth M] , JA [auth N] , KA [auth O] , 
BA [auth H],  CA [auth I],  DA [auth J],  EA [auth K],  GA [auth L],  HA [auth M],  JA [auth N],  KA [auth O],  MA [auth P],  Q [auth A],  S [auth B],  T [auth C],  V [auth D],  W [auth E],  Y [auth F],  Z [auth G]
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.033α = 76.03
b = 112.874β = 71.07
c = 120.009γ = 74.5
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance