Crystal structure of the PIN domain of Saccharomyces cerevisiae Utp23

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain

Lu, J.Sun, M.Ye, K.

(2013) RNA 19: 1815-1824

  • DOI: https://doi.org/10.1261/rna.040808.113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    During synthesis of yeast ribosome, a large complex, called the 90S pre-ribosome or the small subunit processome, is assembled on the nascent precursor rRNA and mediates early processing of 18S rRNA. The Utp23 protein and snR30 H/ACA snoRNA are two conserved components of 90S pre-ribosomes. Utp23 contains a degenerate PIN nuclease domain followed by a long C-terminal tail and associates specifically with snR30. Here, we report the crystal structure of the Utp23 PIN domain at 2.5-Å resolution. The structure reveals a conserved core fold of PIN domain with degenerate active site residues, a unique CCHC Zn-finger motif, and two terminal extension elements. Functional sites of Utp23 have been examined with conservation analysis, mutagenesis, and in vivo and in vitro assays. Mutations in each of three cysteine ligands of zinc, although not the histidine ligand, were lethal or strongly inhibitory to yeast growth, indicating that the Zn-finger motif is required for Utp23 structure or function. The N-terminal helix extension harbors many highly conserved basic residues that mostly are critical for growth and in vitro RNA-binding activity of Utp23. Deletion of the C-terminal tail, which contains a short functionally important sequence motif, disrupted the interaction of Utp23 with snR30 and perturbed the pre-ribosomal association of Utp23. Our data establish a structural framework for dissecting Utp23 function in the assembly and dynamics of 90S pre-ribosomes.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein UTP23
A, B
159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP23YOR004W
Find proteins for Q12339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12339 
Go to UniProtKB:  Q12339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12339
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.427α = 90
b = 91.427β = 90
c = 92.26γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2013-11-06 
  • Deposition Author(s): Lu, J., Ye, K.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations