1UIR

Crystal Structure of Polyamine Aminopropyltransfease from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus

Ohnuma, M.Ganbe, T.Terui, Y.Niitsu, M.Sato, T.Tanaka, N.Tamakoshi, M.Samejima, K.Kumasaka, T.Oshima, T.

(2011) J Mol Biol 408: 971-986

  • DOI: 10.1016/j.jmb.2011.03.025
  • Primary Citation of Related Structures:  
    3ANX, 1UIR

  • PubMed Abstract: 
  • To maintain functional conformations of DNA and RNA in high-temperature environments, an extremely thermophilic bacterium, Thermus thermophilus, employs a unique polyamine biosynthetic pathway and produces more than 16 types of polyamines. In the the ...

    To maintain functional conformations of DNA and RNA in high-temperature environments, an extremely thermophilic bacterium, Thermus thermophilus, employs a unique polyamine biosynthetic pathway and produces more than 16 types of polyamines. In the thermophile genome, only one spermidine synthase homolog (SpeE) was found and it was shown to be a key enzyme in the pathway. The catalytic assay of the purified enzyme revealed that it utilizes triamines (norspermidine and spermidine) and agmatine as acceptors in its aminopropyl transfer reaction; therefore, the enzyme was denoted as a triamine/agmatine aminopropyltransferase (TAAPT). We determined the crystal structures of the enzyme complexed with and without the aminopropyl group donor S-adenosylmethionine. Despite sequence and structural similarity with spermidine synthases from other organisms, a novel C-terminal β-sheet and differences in the catalytic site were observed. The C-terminal module interacts with the gatekeeping loop and fixes the open conformation of the loop to recognize larger polyamine substrates such as agmatine and spermidine. Additional computational docking studies suggest that the structural differences of the catalytic site also contribute to recognition of the aminopropyl/aminobutyl or guanidium moiety of the substrates of TAAPT. These results explain in part the extraordinarily diverse polyamine spectrum found in T. thermophilus.


    Organizational Affiliation

    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan. mioohnuma@rikkyo.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyamine AminopropyltransferaseAB314Thermus thermophilusMutation(s): 0 
EC: 2.5.1.16 (PDB Primary Data), 2.5.1.22 (PDB Primary Data), 2.5.1.104 (UniProt), 2.5.1.126 (UniProt), 2.5.1.79 (UniProt)
Find proteins for Q5SK28 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SK28 
Go to UniProtKB:  Q5SK28
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.775α = 90
b = 87.775β = 90
c = 190.825γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-01-29
    Changes: Database references