3HJY

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

Liang, B.Zhou, J.Kahen, E.Terns, R.M.Terns, M.P.Li, H.

(2009) Nat.Struct.Mol.Biol. 16: 740-746

  • DOI: 10.1038/nsmb.1624
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only ...

    Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 A of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.


    Organizational Affiliation

    Institute of Molecular Biophysics, Tallahassee, Florida, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pseudouridine synthase CBf5
A
327Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: truB
EC: 5.4.99.25
Find proteins for Q7LWY0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q7LWY0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein Nop10
B
53Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: nop10
Find proteins for Q8U1R4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1R4
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3'C21N/A
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (25-MER)D25N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'E14N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.276 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 238.341α = 90.00
b = 238.341β = 90.00
c = 127.369γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
DENZOdata reduction
MOLREPphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description