1TDT

THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1021/bi962522q
  • Primary Citation of Related Structures:  
    1TDT

  • 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-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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
A, B, C
259Mycobacterium tuberculosis variant bovisMutation(s): 0 
UniProt
Find proteins for P56220 (Unknown prokaryotic organism)
Explore P56220 
Go to UniProtKB:  P56220
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56220
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.6α = 90
b = 107.9β = 113
c = 70.7γ = 90
Software Package:
Software NamePurpose
PHASESphasing
TNTrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-05
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references