4FYK

Crystal structure of rcl with 5'-phiosphorothioate-adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the oncoprotein Rcl bound to three nucleotide analogues.

Padilla, A.Amiable, C.Pochet, S.Kaminski, P.A.Labesse, G.

(2013) Acta Crystallogr.,Sect.D 69: 247-255

  • DOI: 10.1107/S0907444912045039
  • Primary Citation of Related Structures:  4FYH, 4FYI
  • Also Cited By: 4KXL, 4KXM, 4KXN, 4P5D, 4P5E

  • PubMed Abstract: 
  • Rcl is a novel N-glycoside hydrolase found in mammals that shows specificity for the hydrolysis of 5'-monophosphate nucleotides. Its role in nucleotide catabolism and the resulting production of 2-deoxyribose 5-phosphate has suggested that it might f ...

    Rcl is a novel N-glycoside hydrolase found in mammals that shows specificity for the hydrolysis of 5'-monophosphate nucleotides. Its role in nucleotide catabolism and the resulting production of 2-deoxyribose 5-phosphate has suggested that it might fuel cancer growth. Its expression is regulated by c-Myc, but its role as an oncoprotein remains to be clarified. In parallel, various nucleosides have been shown to acquire pro-apoptotic properties upon 5'-monophosphorylation in cells. These include triciribine, a tricyclic nucleoside analogue that is currently in clinical trials in combination with a farnesyltransferase inhibitor. Similarly, an N(6)-alkyl-AMP has been shown to be cytotoxic. Interestingly, Rcl has been shown to be inhibited by such compounds in vitro. In order to gain better insight into the precise ligand-recognition determinants, the crystallization of Rcl with these nucleotide analogues was attempted. The first crystal structure of Rcl was solved by molecular replacement using its NMR structure in combination with distantly related crystal structures. The structures of Rcl bound to two other nucleotides were then solved by molecular replacement using the previous crystal structure as a template. The resulting structures, solved at high resolution, led to a clear characterization of the protein-ligand interactions that will guide further rational drug design.


    Organizational Affiliation

    CNRS, UMR5048, Université Montpellier 1 et 2, Centre de Biochimie Structurale, F-34090 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyribonucleoside 5'-monophosphate N-glycosidase
A, B, C, D
152Rattus norvegicusGene Names: Dnph1 (Rcl)
EC: 3.2.2.-
Find proteins for O35820 (Rattus norvegicus)
Go to UniProtKB:  O35820
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SRA
Query on SRA

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE -5'-THIO-MONOPHOSPHATE
C10 H14 N5 O6 P S
UBCPYVAQZGCDJO-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 128.772β = 90.00
c = 57.506γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description