2O06

Human spermidine synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/bi602498k
  • Primary Citation of Related Structures:  2O05, 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine synthase
A, B
304Homo sapiensGene Names: SRM (SPS1, SRML1)
EC: 2.5.1.16
Find proteins for P19623 (Homo sapiens)
Go to Gene View: SRM
Go to UniProtKB:  P19623
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download SDF File 
Download CCD File 
A, B
1,4-DIAMINOBUTANE
PUTRESCINE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
MTA
Query on MTA

Download SDF File 
Download CCD File 
A, B
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.096α = 90.00
b = 135.239β = 90.00
c = 83.321γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
CrystalCleardata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance