4PEH

Dbr1 in complex with synthetic linear RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 debranching enzyme (Dbr1) before they can be metabolized or processed into essential cellular factors, such as snoRNA and miRNA ...

    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, putativeA, C [auth B], E [auth C], G [auth D], I [auth E]356Entamoeba histolyticaMutation(s): 1 
Gene Names: EHI_062730
UniProt
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(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')B [auth V], D [auth W], F [auth X], H [auth Y], J [auth Z]7synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.247 
    • R-Value Work: 0.203 
    • R-Value Observed: 0.206 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 73.021α = 90
    b = 141.936β = 90
    c = 212.942γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-08-27
      Type: Initial release
    • Version 1.1: 2014-10-01
      Changes: Database references
    • Version 1.2: 2017-09-27
      Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy