3Q1R

Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.21 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA.

Reiter, N.J.Osterman, A.Torres-Larios, A.Swinger, K.K.Pan, T.Mondragon, A.

(2010) Nature 468: 784-789

  • DOI: 10.1038/nature09516
  • Primary Citation of Related Structures:  
    3Q1Q, 3Q1R

  • PubMed Abstract: 
  • Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P ...

    Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.


    Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein componentA118Thermotoga maritimaMutation(s): 0 
Gene Names: rnpARNPA OR TM1463RNPBTM_1463
EC: 3.1.26.5
Find proteins for Q9X1H4 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9X1H4 
Go to UniProtKB:  Q9X1H4
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNase P RNAB347N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
TRNA (PHE)C86N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    TRNA 5' LEADERD7N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    B, C
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 4.21 Å
    • R-Value Free: 0.267 
    • R-Value Work: 0.258 
    • R-Value Observed: 0.259 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 169.92α = 90
    b = 169.92β = 90
    c = 185.53γ = 120
    Software Package:
    Software NamePurpose
    MD2data collection
    BUSTERrefinement
    XDSdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-03-09
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance