2A8R: 2.45 Angstrom Crystal Structure Of The Complex Between The Nuclear Snorna Decapping Nudix Hydrolase X29 And Manganese In The Presence Of 7-Methyl-Gtp

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.
PDB ID: 2A8RDownload
MMDB ID: 37963
PDB Deposition Date: 2005/7/8
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.45  Å
Source Organism:
Similar Structures:
Biological Unit for 2A8R: dimeric; determined by author and by software (PISA)
Molecular Components in 2A8R
Label Count Molecule
Proteins (2 molecules)
U8 Snorna-binding Protein X29
Molecule annotation
Chemicals (7 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB