Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.

Wu, H.Min, J.Zeng, H.McCloskey, D.E.Ikeguchi, Y.Loppnau, P.Michael, A.J.Pegg, A.E.Plotnikov, A.N.

(2008) J Biol Chem 283: 16135-16146

  • DOI: https://doi.org/10.1074/jbc.M710323200
  • Primary Citation of Related Structures:  
    3C6K, 3C6M

  • PubMed Abstract: 

    The crystal structures of two ternary complexes of human spermine synthase (EC, one with 5'-methylthioadenosine and spermidine and the other with 5'-methylthioadenosine and spermine, have been solved. They show that the enzyme is a dimer of two identical subunits. Each monomer has three domains: a C-terminal domain, which contains the active site and is similar in structure to spermidine synthase; a central domain made up of four beta-strands; and an N-terminal domain with remarkable structural similarity to S-adenosylmethionine decarboxylase, the enzyme that forms the aminopropyl donor substrate. Dimerization occurs mainly through interactions between the N-terminal domains. Deletion of the N-terminal domain led to a complete loss of spermine synthase activity, suggesting that dimerization may be required for activity. The structures provide an outline of the active site and a plausible model for catalysis. The active site is similar to those of spermidine synthases but has a larger substrate-binding pocket able to accommodate longer substrates. Two residues (Asp(201) and Asp(276)) that are conserved in aminopropyltransferases appear to play a key part in the catalytic mechanism, and this role was supported by the results of site-directed mutagenesis. The spermine synthase.5'-methylthioadenosine structure provides a plausible explanation for the potent inhibition of the reaction by this product and the stronger inhibition of spermine synthase compared with spermidine synthase. An analysis to trace possible evolutionary origins of spermine synthase is also described.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermine synthase
A, B, C, D
381Homo sapiensMutation(s): 0 
Gene Names: SMS
UniProt & NIH Common Fund Data Resources
Find proteins for P52788 (Homo sapiens)
Explore P52788 
Go to UniProtKB:  P52788
PHAROS:  P52788
GTEx:  ENSG00000102172 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52788
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.385α = 94.23
b = 74.032β = 92.88
c = 143.226γ = 107.07
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description