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⇱ RCSB PDB - 3C6K: Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 3C6K | pdb_00003c6k

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.257 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

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 Biological Chem 283: 16135-16146

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

  • PubMed Abstract: 

    The crystal structures of two ternary complexes of human spermine synthase (EC 2.5.1.22), 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.

Macromolecule Content 

  • Total Structure Weight: 173.78 kDa 
  • Atom Count: 12,240 
  • Modeled Residue Count: 1,374 
  • Deposited Residue Count: 1,524 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spermine synthase
A, B, C, D
381Homo sapiensMutation(s): 0 
Gene Names: SMS
EC: 2.5.1.22
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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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.257 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
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
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.