2A8P

2.7 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese

Summary for 2A8P

• Entry DOI: 10.2210/pdb2a8p/pdb
• Related: 1U20 2A8Q 2A8R 2A8S 2A8T
• Descriptor: U8 snoRNA-binding protein X29, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: modified nudix hydrolase fold, hydrolase
• Biological source: Xenopus laevis (African clawed frog)
• Total number of polymer chains: 2
• Total formula weight: 49113.90

Authors

Scarsdale, J.N.,Peculis, B.A.,Wright, H.T. (deposition date: 2005-07-08, release date: 2006-03-28, Last modification date: 2023-08-23)

Primary citation

Scarsdale, J.N.,Peculis, B.A.,Wright, H.T.
Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes
Structure, 14:331-343, 2006

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.

PubMed: 16472752
DOI: 10.1016/j.str.2005.11.010

Experimental method

X-RAY DIFFRACTION (2.7 Å)