Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 173.78 kDa 
• Atom Count: 12240 
• Residue Count: 1374 
• Unique protein chains: 1

3C6K

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

• DOI: 10.2210/pdb3C6K/pdb
• Entry: 3C6K supersedes: 2QFM

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-04 Released: 2008-02-19 
• Deposition Author(s): Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Pegg, A.E., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.257 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

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 Biol Chem 283: 16135-16146

• PubMed: 18367445 
• DOI: 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermine synthase	A, B, C, D	381	Homo sapiens	Mutation(s): 0  Gene Names: SMS EC: 2.5.1.22
Find proteins for P52788 (Homo sapiens) Explore P52788  Go to UniProtKB:  P52788
NIH Common Fund Data Resources
PHAROS  P52788 GTEx  ENSG00000102172

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	A, B, C, D	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
SPD	A, B, C, D	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MTA	Ki:  300   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 43.385	α = 94.23
b = 74.032	β = 92.88
c = 143.226	γ = 107.07

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-04 
• Released Date: 2008-02-19 
Deposition Author(s): Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Pegg, A.E., Plotnikov, A.N., Structural Genomics Consortium (SGC)
• This entry supersedes: 2QFM

Revision History 

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance