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 

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:  

  • 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
356Entamoeba histolyticaMutation(s): 1 
Find proteins for C4M1P9 (Entamoeba histolytica)
Go to UniProtKB:  C4M1P9
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*AP*AP*CP*A)-3')V,W,X,Y,Z5synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*(G46)P*U)-3')Q,R,S,T,U2synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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

Download SDF File 
Download CCD File 
A, B, C, D, E
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
G46
Query on G46
Q, R, S, T, U
RNA LINKINGC10 H14 N5 O7 P SG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.037α = 90.00
b = 142.479β = 90.00
c = 214.665γ = 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: 2014-11-12
    Type: Atomic model, Derived calculations
  • Version 1.3: 2015-02-25
    Type: Non-polymer description
  • Version 1.4: 2017-09-27
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary