4GCW

Crystal structure of RNase Z in complex with precursor tRNA(Thr)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Activation of tRNA Maturation by Downstream Uracil Residues in B. subtilis

Pellegrini, O.Li de la Sierra-Gallay, I.Piton, J.Gilet, L.Condon, C.

(2012) Structure 20: 1769-1777

  • DOI: 10.1016/j.str.2012.08.002

  • PubMed Abstract: 
  • Ribonuclease (RNase) Z is involved in the maturation of the 3' ends of transfer RNAs (tRNAs) in all three kingdoms of life. To prevent futile cycles of CCA addition and removal, eukaryotic RNase Z discriminates against mature tRNAs bearing a CCA moti ...

    Ribonuclease (RNase) Z is involved in the maturation of the 3' ends of transfer RNAs (tRNAs) in all three kingdoms of life. To prevent futile cycles of CCA addition and removal, eukaryotic RNase Z discriminates against mature tRNAs bearing a CCA motif, with the first cytosine residue (C74) being the key antideterminant. Here, we show that, remarkably, the B. subtilis enzyme does not discriminate against cytosine in position 74, but rather is highly stimulated by uracil in this location. Consistent with this observation, the vast majority of B. subtilis tRNA precursor substrates of RNase Z naturally contain U74. Those tRNA precursors with a uracil further downstream are also substrates for RNase Z, but are matured in a two-step endo/exonuclease reaction. We solved the first crystal structure of B. subtilis RNase Z bound to a tRNA(Thr) precursor with U74 and show that the enzyme has a specific binding pocket for this nucleotide.


    Organizational Affiliation

    CNRS UPR 9073 (affiliated with Université Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease Z
A
320Bacillus subtilis (strain 168)Mutation(s): 2 
Gene Names: rnz (yqjK)
EC: 3.1.26.11
Find proteins for P54548 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P54548
Entity ID: 2
MoleculeChainsLengthOrganism
TRNA(THR)B76N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
B
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
B
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.080α = 90.00
b = 42.550β = 127.18
c = 110.890γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XSCALEdata scaling
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release