2O07

Human spermidine synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine synthase
A, B
304Homo sapiensMutation(s): 0 
Gene Names: SRMSPS1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19623
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.125α = 90
b = 60.663β = 108.68
c = 86.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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