3TDT

COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINO-6-OXOPIMELATE AND COENZYME A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.

Beaman, T.W.Blanchard, J.S.Roderick, S.L.

(1998) Biochemistry 37: 10363-10369

  • DOI: 10.1021/bi980759b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetrahydrodipicolinate (THDP) N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to L-2-(succinylamino)-6-oxopimelate and CoA. This reaction represents the committed step of the succinylase branch of the diamino ...

    Tetrahydrodipicolinate (THDP) N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to L-2-(succinylamino)-6-oxopimelate and CoA. This reaction represents the committed step of the succinylase branch of the diaminopimelate/L-lysine biosynthetic pathway by which many bacteria synthesize meso-diaminopimelate, a component of peptidoglycan, and L-lysine from L-aspartate. The crystal structures of THDP succinyltransferase in complex with the substrate/cofactor pairs L-2-aminopimelate/coenzyme A and L-2-amino-6-oxopimelate/coenzyme A have been determined and refined to 2.0 A resolution. The active site of the enzyme is a long narrow groove located at the interface between two left-handed parallel beta-helix (LbetaH) structural domains of the trimeric enzyme. On binding the amino acid acceptor and cofactor, this groove is covered by residues from the C-terminus of one subunit and a flexible loop excluded from the LbetaH domain of an adjacent subunit to form a tunnel. This conformational change is directly related to interactions between the enzyme and the bound amino acid substrate and cofactor and serves to shield the ligands from bulk solvent and to orient the nucleophilic amino group of the amino acid acceptor toward the mercaptoethylamine group of the cofactor.


    Related Citations: 
    • Three-Dimensional Structure of Tetrahydrodipicolinate N-Succinyltransferase
      Beaman, T.W.,Binder, D.A.,Blanchard, J.S.,Roderick, S.L.
      (1997) Biochemistry 36: 489
    • 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
274Unknown prokaryotic organismMutation(s): 0 
Gene Names: dapD
EC: 2.3.1.117
Find proteins for P56220 (Unknown prokaryotic organism)
Go to UniProtKB:  P56220
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
26P
Query on 26P

Download SDF File 
Download CCD File 
A
2-AMINO-6-OXOPIMELIC ACID
C7 H11 N O5
UKCSFKLWNHUBDY-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.152 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 96.000α = 90.00
b = 96.000β = 90.00
c = 72.300γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement
X-PLORrefinement
XDSdata reduction
X-PLORmodel building
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance