1TDT

THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase.

Beaman, T.W.Binder, D.A.Blanchard, J.S.Roderick, S.L.

(1997) Biochemistry 36: 489-494

  • DOI: 10.1021/bi962522q

  • PubMed Abstract: 
  • The conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA is catalyzed by tetrahydrodipicolinate N-succinyltransferase and is the committed step in the succinylase pathway by which bacteria synthesize L-lys ...

    The conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA is catalyzed by tetrahydrodipicolinate N-succinyltransferase and is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The X-ray crystal structure of THDP succinyltransferase has been determined to 2.2 A resolution and has been refined to a crystallographic R-factor of 17.0%. The enzyme is trimeric and displays the left-handed parallel beta-helix (L beta H) structural motif encoded by the "hexapeptide repeat" amino acid sequence motif [Raetz, C.R.H., & Roderick, S.L. (1995) Science 270, 997-1000]. The approximate location of the active site of THDP succinyltransferase is suggested by the proximity of binding sites for two inhibitors: p-(chloromercuri)benzenesulfonic acid and cobalt ion, both of which bind to the L beta H domain.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Tetrahydrodipicolinate-N-Succinyltransferase
      Binder, D.A.,Blanchard, J.S.,Roderick, S.L.
      (1996) Proteins 26: 115


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
A, B, C
259Unknown prokaryotic organismMutation(s): 0 
Gene Names: dapD
EC: 2.3.1.117
Find proteins for P56220 (Unknown prokaryotic organism)
Go to UniProtKB:  P56220
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.600α = 90.00
b = 107.900β = 113.00
c = 70.700γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
XSCALEdata scaling
XDSdata reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-05
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance