2A8Q

2.6 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2A8P, 2A8T, 2A8S, 2A8R, 2A8Q

  • 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 nucleo-t(s)ide-assisted Mn(+2) uptake account for the observed cooperativity of metal binding ...

    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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U8 snoRNA-binding protein X29 AB212Xenopus laevisMutation(s): 1 
Gene Names: nudt16
EC: 3.6.1 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
Find proteins for Q6TEC1 (Xenopus laevis)
Explore Q6TEC1 
Go to UniProtKB:  Q6TEC1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A,BL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.828α = 90
b = 82.284β = 90
c = 111.86γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description