2A8S

2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1016/j.str.2005.11.010
  • Primary Citation of Related Structures:  
    2A8P, 2A8Q, 2A8R, 2A8S, 2A8T

  • 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. 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U8 snoRNA-binding protein X29
A, B
212Xenopus laevisMutation(s): 2 
EC: 3.6.1 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
UniProt
Find proteins for Q6TEC1 (Xenopus laevis)
Explore Q6TEC1 
Go to UniProtKB:  Q6TEC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TEC1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A, B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.998α = 90
b = 82.553β = 90
c = 112.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description