2A8T

2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes

Scarsdale, J.N.Peculis, B.A.Wright, H.T.

(2006) Structure 14: 331-343

  • DOI: 10.1016/j.str.2005.11.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X29, a 25 kDa Nudix hydrolase from Xenopus laevis that cleaves 5' caps from U8 snoRNA, crystallizes as a homodimeric apoenzyme. Manganese binds crystals of apo-X29 to form holo-X29 only in the presence of nucleot(s)ide. Structural changes in X29 on n ...

    X29, a 25 kDa Nudix hydrolase from Xenopus laevis that cleaves 5' caps from U8 snoRNA, crystallizes as a homodimeric apoenzyme. Manganese binds crystals of apo-X29 to form holo-X29 only in the presence of nucleot(s)ide. Structural changes in X29 on nucleo-t(s)ide-assisted Mn(+2) uptake account for the observed cooperativity of metal binding. Structures of X29 with GTP or m7GpppA show a different mode of ligand binding from that of other cap binding proteins and suggest a possible three- or four-metal Nudix reaction mechanism. The X29 dimer has no known RNA binding motif, but its striking surface dipolarity and unique structural features create a plausible RNA binding channel on the positive face of the protein. Because U8 snoRNP is essential for accumulation of mature 5.8S and 28S rRNA in vertebrate ribosome biogenesis, and cap structures are required for U8 stability in vivo, X29 could profoundly influence this fundamental cellular pathway.


    Related Citations: 
    • Crystals of X29, a Xenopus Laevis U8 SnoRNA Binding Protein with Nuclear Decapping Activity
      Peculis, B.A.,Scarsdale, J.N.,Wright, H.T.
      (2004) Acta Crystallogr.,Sect.D 60: 1668
    • Xenopus U8 SnoRNA Binding Protein is a Conserved Nuclear Decapping Enzyme
      Ghosh, T.,Peterson, B.,Tomasevic, N.,Peculis, B.A.
      (2004) Mol.Cell 13: 817


    Organizational Affiliation

    Department of Biochemistry and Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, Virginia 23219, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U8 snoRNA-binding protein X29
A, B
212Xenopus laevisMutation(s): 0 
Gene Names: nudt16
EC: 3.6.1.62
Find proteins for Q6TEC1 (Xenopus laevis)
Go to UniProtKB:  Q6TEC1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MGT
Query on MGT

Download SDF File 
Download CCD File 
A, B
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.702α = 90.00
b = 81.710β = 90.00
c = 111.706γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
CNSphasing
d*TREKdata scaling
REFMACrefinement
CrystalCleardata reduction
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance