ISDA

Deposition Date 2005-07-08

Release Date 2006-03-28

Last Version Date 2023-08-23

Entry Detail

PDB ID:

2A8Q

Keywords:

TRANSLATION,HYDROLASE

Title:

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

Biological Source:

Source Organism:

Xenopus laevis (Taxon ID: 8355)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.25

R-Value Work:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:U8 snoRNA-binding protein X29
Chain IDs:A, B
Chain Length:212
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:Q6TEC1 Pfam ID:PF22327

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
YCM	A	CYS	S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

Ligand Molecules

POP

Primary Citation

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

Scarsdale, J.N, Peculis, B.A, Wright, H.T, Peculis, B.A, Scarsdale, J.N, Wright, H.T, Ghosh, T, Peterson, B, Tomasevic, N, Peculis, B.A.Show

Structure 14 331 343 (2006)

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

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures