2LCQ

Solution structure of the endonuclease Nob1 from P.horikoshii

Summary for 2LCQ

• Entry DOI: 10.2210/pdb2lcq/pdb
• NMR Information: BMRB: 17595
• Descriptor: Putative toxin VapC6, ZINC ION (2 entities in total)
• Functional Keywords: pin domain, zn ribbon domain, ribosome biogenesis, metal binding protein
• Biological source: Pyrococcus horikoshii (Euryarchaeotes)
• Total number of polymer chains: 1
• Total formula weight: 18397.90

Authors

Veith, T.,Martin, R.,Wurm, J.P.,Weis, B.,Duchardt-Ferner, E.,Safferthal, C.,Hennig, R.,Mirus, O.,Bohnsack, M.T.,Woehnert, J.,Schleiff, E. (deposition date: 2011-05-05, release date: 2011-12-14, Last modification date: 2024-05-01)

Primary citation

Veith, T.,Martin, R.,Wurm, J.P.,Weis, B.L.,Duchardt-Ferner, E.,Safferthal, C.,Hennig, R.,Mirus, O.,Bohnsack, M.T.,Wohnert, J.,Schleiff, E.
Structural and functional analysis of the archaeal endonuclease Nob1.
Nucleic Acids Res., 40:3259-3274, 2012

PubMed Abstract: Eukaryotic ribosome biogenesis requires the concerted action of numerous ribosome assembly factors, for most of which structural and functional information is currently lacking. Nob1, which can be identified in eukaryotes and archaea, is required for the final maturation of the small subunit ribosomal RNA in yeast by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Here, we show that this also holds true for Nob1 from the archaeon Pyrococcus horikoshii, which efficiently cleaves RNA-substrates containing the D-site of the preribosomal RNA in a manganese-dependent manner. The structure of PhNob1 solved by nuclear magnetic resonance spectroscopy revealed a PIN domain common with many nucleases and a zinc ribbon domain, which are structurally connected by a flexible linker. We show that amino acid residues required for substrate binding reside in the PIN domain whereas the zinc ribbon domain alone is sufficient to bind helix 40 of the small subunit rRNA. This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site.

PubMed: 22156373
DOI: 10.1093/nar/gkr1186

Experimental method

SOLUTION NMR