1F8Y

CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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

  • DOI: 10.1016/s0969-2126(96)00013-5
  • Primary Citation of Related Structures:  
    1F8X, 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 acceptor purine or pyrimidine base ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASEA, B157Lactobacillus leichmanniiMutation(s): 0 
Gene Names: ntd
EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii)
Explore Q9R5V5 
Go to UniProtKB:  Q9R5V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R5V5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5MD
Query on 5MD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2'-deoxy-1-methyl-pseudouridine
C10 H14 N2 O5
AMDJRICBYOAHBZ-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.6α = 90
b = 149.6β = 90
c = 149.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance