4PEF

Dbr1 in complex with sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA lariat debranching enzyme, putative
A, B, C, D, E
360Entamoeba histolyticaMutation(s): 0 
Find proteins for C4M1P9 (Entamoeba histolytica)
Go to UniProtKB:  C4M1P9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B, C, D, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.217α = 90.00
b = 141.694β = 90.00
c = 213.216γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy