Solution structure of the endonuclease Nob1 from P.horikoshii

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

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This is version 1.1 of the entry. See complete history


Structural and functional analysis of the archaeal endonuclease Nob1.

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.

(2012) Nucleic Acids Res 40: 3259-3274

  • DOI: https://doi.org/10.1093/nar/gkr1186
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Institute for Molecular Biosciences, Johann-Wolfgang-Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative toxin VapC6165Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: vapC6PH0709
Find proteins for O58440 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58440 
Go to UniProtKB:  O58440
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58440
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references