3BXY

Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Escherichia coli tetrahydrodipicolinate N-succinyltransferase reveals the role of a conserved C-terminal helix in cooperative substrate binding.

Nguyen, L.Kozlov, G.Gehring, K.

(2008) Febs Lett. 582: 623-626

  • DOI: 10.1016/j.febslet.2008.01.032

  • PubMed Abstract: 
  • Tetrahydrodipicolinate N-succinyltransferase is an enzyme present in many bacteria that catalyzes the first step of the succinylase pathway for the synthesis of meso-diaminopimelate and the amino acid L-lysine. Inhibition of the synthesis of meso-dia ...

    Tetrahydrodipicolinate N-succinyltransferase is an enzyme present in many bacteria that catalyzes the first step of the succinylase pathway for the synthesis of meso-diaminopimelate and the amino acid L-lysine. Inhibition of the synthesis of meso-diaminopimelate, a component of peptidoglycan present in the cell wall of bacteria, is a potential route for the development of novel anti-bacterial agents. Here, we report the crystal structure of the DapD tetrahydrodipicolinate N-succinyltransferase from Escherichia coli at 2.0 A resolution. Comparison of the structure with the homologous enzyme from Mycobacterium bovis reveals the C-terminal helix undergoes a large rearrangement upon substrate binding, which contributes to cooperativity in substrate binding.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, 3655 Promenade Sir William Osler, Québec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
A
285Escherichia coli O157:H7Mutation(s): 0 
Gene Names: dapD
EC: 2.3.1.117
Find proteins for Q8X8Y7 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X8Y7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 102.924α = 90.00
b = 102.924β = 90.00
c = 69.229γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance