3BK2

Crystal Structure Analysis of the RNase J/UMP complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural insights into the dual activity of RNase J

de la Sierra-Gallay, I.L., Zig, L., Jamalli, A., Putzer, H.

(2008) Nat Struct Mol Biol 15: 206-212

  • DOI: 10.1038/nsmb.1376
  • Primary Citation of Related Structures:  
    3BK1, 3BK2

  • PubMed Abstract: 

    • The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E-like endoribonucleolytic and a 5'-to-3' exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown ...

    The maturation and stability of RNA transcripts is controlled by a combination of endo- and exoRNases. RNase J is unique, as it combines an RNase E-like endoribonucleolytic and a 5'-to-3' exoribonucleolytic activity in a single polypeptide. The structural basis for this dual activity is unknown. Here we report the crystal structures of Thermus thermophilus RNase J and its complex with uridine 5'-monophosphate. A binding pocket coordinating the phosphate and base moieties of the nucleotide in the vicinity of the catalytic center provide a rationale for the 5'-monophosphate-dependent 5'-to-3' exoribonucleolytic activity. We show that this dependence is strict; an initial 5'-PPP transcript cannot be degraded exonucleolytically from the 5'-end. Our results suggest that RNase J might switch promptly from endo- to exonucleolytic mode on the same RNA, a property that has important implications for RNA metabolism in numerous prokaryotic organisms and plant organelles containing RNase J orthologs.

    Organizational Affiliation: 

    FRC550, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metal dependent hydrolaseA562Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TTC0775, rnj, TT_C0775
EC: 3 (PDB Primary Data), 3.1 (UniProt)
Find proteins for Q72JJ7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72JJ7 
Go to UniProtKB:  Q72JJ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P
Download Ideal Coordinates CCD File 
 E [auth A]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 F [auth A], G [auth A], H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.227 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.08α = 90
b = 118β = 90
c = 228.32γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance