2B2C

Cloning, expression, characterisation and three- dimensional structure determination of the Caenorhabditis elegans spermidine synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cloning, expression, characterisation and three-dimensional structure determination of Caenorhabditis elegans spermidine synthase

Dufe, V.T.Luersen, K.Eschbach, M.L.Haider, N.Karlberg, T.Walter, R.D.Al-Karadaghi, S.

(2005) FEBS LETT. 579: 6037-6043

  • DOI: 10.1016/j.febslet.2005.09.050

  • PubMed Abstract: 
  • The polyamine synthesis enzyme spermidine synthase (SPDS) has been cloned from the model nematode Caenorhabditis elegans. Biochemical characterisation of the recombinantly expressed protein revealed a high degree of similarity to other eukaryotic SPD ...

    The polyamine synthesis enzyme spermidine synthase (SPDS) has been cloned from the model nematode Caenorhabditis elegans. Biochemical characterisation of the recombinantly expressed protein revealed a high degree of similarity to other eukaryotic SPDS with the exception of a low affinity towards the substrate decarboxylated S-adenosylmethionine (Km = 110 microM) and a less pronounced feedback inhibition by the second reaction product 5'-methylthioadenosine (IC50 = 430 microM). The C. elegans protein that carries a nematode-specific insertion of 27 amino acids close to its N-terminus was crystallized, leading to the first X-ray structure of a dimeric eukaryotic SPDS.


    Organizational Affiliation

    Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
spermidine synthase
A, B
314Caenorhabditis elegansMutation(s): 0 
Gene Names: spds-1 (spds)
EC: 2.5.1.16
Find proteins for G5EFG3 (Caenorhabditis elegans)
Go to UniProtKB:  G5EFG3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.990α = 90.00
b = 99.230β = 107.20
c = 67.850γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description