2B2C | pdb_00002b2c

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

• PDB DOI: https://doi.org/10.2210/pdb2B2C/pdb

• Classification: TRANSFERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-19 Released: 2005-11-15 
• Deposition Author(s): Dufe, V.T., Luersen, K., Eschbach, M.L., Haider, N., Karlberg, T., Walter, R.D., Al-Karadaghi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

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

• PubMed: 16226262 
• DOI: https://doi.org/10.1016/j.febslet.2005.09.050
• Primary Citation of Related Structures:  
  2B2C


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.14 kDa 
• Atom Count: 4,462 
• Modelled Residue Count: 552 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
spermidine synthase	A, B	314	Caenorhabditis elegans	Mutation(s): 0  EC: 2.5.1.16
UniProt
Find proteins for G5EFG3 (Caenorhabditis elegans) Explore G5EFG3  Go to UniProtKB:  G5EFG3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.99	α = 90
b = 99.23	β = 107.2
c = 67.85	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-15 
Deposition Author(s): Dufe, V.T., Luersen, K., Eschbach, M.L., Haider, N., Karlberg, T., Walter, R.D., Al-Karadaghi, S.

Revision History  

• Version 1.0: 2005-11-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Refinement description