2O06

Human spermidine synthase

• PDB DOI: https://doi.org/10.2210/pdb2O06/pdb

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


• Deposited: 2006-11-27 Released: 2006-12-12 
• Deposition Author(s): Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Structure and mechanism of spermidine synthases.

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

(2007) Biochemistry 46: 8331-8339

• PubMed: 17585781 
• DOI: https://doi.org/10.1021/bi602498k
• Primary Citation of Related Structures:  
  2O05, 2O06, 2O07, 2O0L


• PubMed Abstract: 
  

  Aminopropyltransferases transfer aminopropyl groups from decarboxylated S-adenosylmethionine to amine acceptors, forming polyamines. Structural and biochemical studies have been carried out with the human spermidine synthase, which is highly specific for putrescine as the amine acceptor, and the Thermotoga maritima spermidine synthase, which prefers putrescine but is more tolerant of other substrates. Comparison of the structures of the human spermidine synthase with both substrates and products with the known structure of T. maritima spermidine synthase complexed to a multisubstrate analogue inhibitor and analysis of the properties of site-directed mutants provide a general mechanistic hypothesis for the aminopropyl transfer reaction. The studies also provide a structural basis for the specificity of the spermidine synthase subclass of the aminopropyltransferase family.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario, M5G 1L5, Canada.

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: 68.85 kDa 
• Atom Count: 5,150 
• Modelled Residue Count: 586 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B	304	Homo sapiens	Mutation(s): 0  Gene Names: SRM, SPS1 EC: 2.5.1.16
UniProt & NIH Common Fund Data Resources
Find proteins for P19623 (Homo sapiens) Explore P19623  Go to UniProtKB:  P19623
PHAROS:  P19623 GTEx:  ENSG00000116649

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	E [auth A], H [auth B]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
PUT	F [auth A], I [auth B]	1,4-DIAMINOBUTANE C4 H12 N2 KIDHWZJUCRJVML-UHFFFAOYSA-N
MG	C [auth A], D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.096	α = 90
b = 135.239	β = 90
c = 83.321	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-12-12
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations