3BXY | pdb_00003bxy

Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.205 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 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: https://doi.org/10.1016/j.febslet.2008.01.032
  • Primary Citation Related Structures: 
    3BXY

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 31.11 kDa 
  • Atom Count: 2,294 
  • Modeled Residue Count: 275 
  • Deposited Residue Count: 285 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase285Escherichia coli O157:H7Mutation(s): 0 
Gene Names: dapD
EC: 2.3.1.117
UniProt
Find proteins for Q8X8Y7 (Escherichia coli O157:H7)
Explore Q8X8Y7 
Go to UniProtKB:  Q8X8Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X8Y7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.205 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.924α = 90
b = 102.924β = 90
c = 69.229γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description