3CPR

The crystal structure of Corynebacterium glutamicum dihydrodipicolinate synthase to 2.2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein.

Rice, E.A.Bannon, G.A.Glenn, K.C.Jeong, S.S.Sturman, E.J.Rydel, T.J.

(2008) Arch.Biochem.Biophys. 480: 111-121

  • DOI: 10.1016/j.abb.2008.09.018

  • PubMed Abstract: 
  • The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS ...

    The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.


    Organizational Affiliation

    Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, MO 63167, USA. elena.a.rice@monsanto.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrodipicolinate synthetase
A, B
304Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)Mutation(s): 0 
Gene Names: dapA
EC: 4.3.3.7
Find proteins for P19808 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  P19808
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A, B
L-peptide linkingC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.300α = 90.00
b = 54.810β = 129.39
c = 98.610γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNXrefinement
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 2.0: 2018-05-30
    Type: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary