1F8X

CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.

Armstrong, S.R.Cook, W.J.Short, S.A.Ealick, S.E.

(1996) Structure 4: 97-107

  • Primary Citation of Related Structures:  1F8Y

  • PubMed Abstract: 
  • Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an ac ...

    Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. The kinetics describe a ping-pong-bi-bi pathway involving the formation of a covalent enzyme-deoxyribose intermediate. The enzyme is produced by a limited number of microorganisms and its functions have been exploited in its use as a biocatalyst to synthesize nucleoside analogs of therapeutic interest.


    Related Citations: 
    • Crystallization and Preliminary X-ray Investigation of Recombinant Lactobacillus leichmannii Nucleoside Deoxyribosyltransferase
      Cook, W.J.,Short, S.A.,Ealick, S.E.
      (1990) J.Biol.Chem. 265: 2682


    Organizational Affiliation

    Section of Biochemistry, Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
A, B
157Lactobacillus leichmanniiGene Names: ntd
EC: 2.4.2.6
Find proteins for Q9R5V5 (Lactobacillus leichmannii)
Go to UniProtKB:  Q9R5V5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.166 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 151.000α = 90.00
b = 151.000β = 90.00
c = 151.000γ = 90.00
Software Package:
Software NamePurpose
SDMSdata reduction
PHASESphasing
SDMSdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance