3OIJ

Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

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This is version 1.3 of the entry. See complete history


Literature

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.

Thomas, S.R.Keller, C.A.Szyk, A.Cannon, J.R.Laronde-Leblanc, N.A.

(2011) Nucleic Acids Res 39: 2445-2457

  • DOI: https://doi.org/10.1093/nar/gkq1131
  • Primary Citation of Related Structures:  
    3O7B, 3OII, 3OIJ, 3OIN

  • PubMed Abstract: 

    Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen-Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Essential for mitotic growth 1
A, B
253Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06287 
Go to UniProtKB:  Q06287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06287
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'
C, D
14N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.377α = 90
b = 91.86β = 90
c = 96.931γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description