5YZ4

Structure of the PIN domain endonuclease Utp24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.228 

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This is version 2.2 of the entry. See complete history


Literature

Structural and functional analysis of Utp24, an endonuclease for processing 18S ribosomal RNA.

An, W.Du, Y.Ye, K.

(2018) PLoS One 13: e0195723-e0195723

  • DOI: https://doi.org/10.1371/journal.pone.0195723
  • Primary Citation of Related Structures:  
    5YZ4

  • PubMed Abstract: 

    The precursor ribosomal RNA is processed by multiple steps of nucleolytic cleavage to generate mature rRNAs. Utp24 is a PIN domain endonuclease in the early 90S precursor of small ribosomal subunit and is proposed to cleave at sites A1 and A2 of pre-rRNA. Here we determine the crystal structure of Utp24 from Schizosaccharomyces pombe at 2.1 angstrom resolution. Utp24 structurally resembles the ribosome assembly factor Utp23 and both contain a Zn-finger motif. Functional analysis in Saccharomyces cerevisiae shows that depletion of Utp24 disturbs the assembly of 90S and abolishes cleavage at sites A0, A1 and A2. The 90S assembled with inactivated Utp24 is arrested at a post-A0-cleavage state and contains enriched nuclear exosome for degradation of 5' ETS. Despite of high sequence conservation, Utp24 from other organisms is unable to form an active 90S in S. cerevisiae, suggesting that Utp24 needs to be precisely positioned in 90S. Our study provides biochemical and structural insight into the role of Utp24 in 90S assembly and activity.


  • Organizational Affiliation

    College of Biological Sciences, China Agricultural University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein fcf1133Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: fcf1
UniProt
Find proteins for O13610 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13610 
Go to UniProtKB:  O13610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13610
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.74α = 90
b = 73.328β = 90
c = 74.262γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31430024

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 2.0: 2019-02-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 2.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description