4BY9

The structure of the Box CD enzyme reveals regulation of rRNA methylation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Structure of the Box C/D Enzyme Reveals Regulation of RNA Methylation.

Lapinaite, A.Simon, B.Skjaerven, L.Rakwalska-Bange, M.Gabel, F.Carlomagno, T.

(2013) Nature 502: 519

  • DOI: 10.1038/nature12581

  • PubMed Abstract: 
  • Post-transcriptional modifications are essential to the cell life cycle, as they affect both pre-ribosomal RNA processing and ribosome assembly. The box C/D ribonucleoprotein enzyme that methylates ribosomal RNA at the 2'-O-ribose uses a multitude of ...

    Post-transcriptional modifications are essential to the cell life cycle, as they affect both pre-ribosomal RNA processing and ribosome assembly. The box C/D ribonucleoprotein enzyme that methylates ribosomal RNA at the 2'-O-ribose uses a multitude of guide RNAs as templates for the recognition of rRNA target sites. Two methylation guide sequences are combined on each guide RNA, the significance of which has remained unclear. Here we use a powerful combination of NMR spectroscopy and small-angle neutron scattering to solve the structure of the 390‚ÄČkDa archaeal RNP enzyme bound to substrate RNA. We show that the two methylation guide sequences are located in different environments in the complex and that the methylation of physiological substrates targeted by the same guide RNA occurs sequentially. This structure provides a means for differential control of methylation levels at the two sites and at the same time offers an unexpected regulatory mechanism for rRNA folding.


    Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NOP5/NOP56 RELATED PROTEIN
C, F, I, L
366Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)N/A
Find proteins for Q8U4M1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U4M1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L7AE
D, G, J, M
121Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Gene Names: rpl7ae
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U160
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
E, H, K, N
227Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Gene Names: flpA
EC: 2.1.1.-
Find proteins for Q8U4M2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U4M2
Entity ID: 1
MoleculeChainsLengthOrganism
SSR26A,B72Pyrococcus furiosus
Entity ID: 5
MoleculeChainsLengthOrganism
5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'W,X,Y,Z11Pyrococcus furiosus
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Atomic model
  • Version 1.2: 2013-10-23
    Type: Database references
  • Version 1.3: 2013-10-30
    Type: Database references
  • Version 1.4: 2016-05-04
    Type: Atomic model, Other