4PEI

Dbr1 in complex with synthetic branched RNA analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1.

Montemayor, E.J.Katolik, A.Clark, N.E.Taylor, A.B.Schuermann, J.P.Combs, D.J.Johnsson, R.Holloway, S.P.Stevens, S.W.Damha, M.J.Hart, P.J.

(2014) Nucleic Acids Res 42: 10845-10855

  • DOI: 10.1093/nar/gku725
  • Primary Citation of Related Structures:  
    4PEF, 4PEG, 4PEH, 4PEI

  • PubMed Abstract: 
  • The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2',5'-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debra ...

    The enzymatic processing of cellular RNA molecules requires selective recognition of unique chemical and topological features. The unusual 2',5'-phosphodiester linkages in RNA lariats produced by the spliceosome must be hydrolyzed by the intron debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA. Dbr1 is also involved in the propagation of retrotransposons and retroviruses, although the precise role played by the enzyme in these processes is poorly understood. Here, we report the first structures of Dbr1 alone and in complex with several synthetic RNA compounds that mimic the branchpoint in lariat RNA. The structures, together with functional data on Dbr1 variants, reveal the molecular basis for 2',5'-phosphodiester recognition and explain why the enzyme lacks activity toward 3',5'-phosphodiester linkages. The findings illuminate structure/function relationships in a unique enzyme that is central to eukaryotic RNA metabolism and set the stage for the rational design of inhibitors that may represent novel therapeutic agents to treat retroviral infections and neurodegenerative disease.


    Organizational Affiliation

    Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, TX 78229, USA Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, USA pjhart1@biochem.uthscsa.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA lariat debranching enzyme, putativeABCDE356Entamoeba histolyticaMutation(s): 1 
Gene Names: EHI_062730
Find proteins for C4M1P9 (Entamoeba histolytica)
Explore C4M1P9 
Go to UniProtKB:  C4M1P9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*AP*AP*CP*A)-3')V, W, X, Y, Z5synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*(G46)P*U)-3')Q, R, S, T, U2synthetic construct
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PG4
      Query on PG4

      Download CCD File 
      B
      TETRAETHYLENE GLYCOL
      C8 H18 O5
      UWHCKJMYHZGTIT-UHFFFAOYSA-N
       Ligand Interaction
      SO4
      Query on SO4

      Download CCD File 
      A, B, C, D, E
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      GOL
      Query on GOL

      Download CCD File 
      A, C, D
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      NI
      Query on NI

      Download CCD File 
      A, B, C, D, E
      NICKEL (II) ION
      Ni
      VEQPNABPJHWNSG-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.95 Å
      • R-Value Free: 0.229 
      • R-Value Work: 0.184 
      • R-Value Observed: 0.186 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 73.037α = 90
      b = 142.479β = 90
      c = 214.665γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2014-08-27
        Type: Initial release
      • Version 1.1: 2014-10-01
        Changes: Database references
      • Version 1.2: 2014-11-12
        Changes: Atomic model, Derived calculations
      • Version 1.3: 2015-02-25
        Changes: Non-polymer description
      • Version 1.4: 2017-09-27
        Changes: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary