3OIN

Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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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: 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 ...

    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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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1A, B253Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EMG1, NEP1, YLR186W, L9470.5
EC: 2.1.1.260
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06287 
Go to UniProtKB:  Q06287
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'C14Saccharomyces cerevisiae
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SAH (Subject of Investigation/LOI)
    Query on SAH
    Download Ideal Coordinates CCD File 
    		 F [auth B]S-ADENOSYL-L-HOMOCYSTEINE
    C14 H20 N6 O5 S
    ZJUKTBDSGOFHSH-WFMPWKQPSA-N    		 Ligand Interaction
    GOL
    Query on GOL
    Download Ideal Coordinates CCD File 
    		 D [auth A], E [auth A]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N    		 Ligand Interaction
    CL
    Query on CL
    Download Ideal Coordinates CCD File 
    		 H [auth C]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    		 G [auth C]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    SCY
    Query on SCY    		A, BL-PEPTIDE LINKINGC5 H9 N O3 SCYS
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.230 
    • R-Value Work: 0.192 
    • R-Value Observed: 0.194 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.774α = 90
    b = 88.749β = 90
    c = 115.751γ = 90
    Software Package:
    Software NamePurpose
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    HKL-2000data reduction
    HKL-2000data scaling
    MOLREPphasing

    Structure Validation

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    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 2.0: 2020-04-22
      Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary