4GCW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

Starting Model: experimental
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This is version 1.1 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: https://doi.org/10.1016/j.str.2012.08.002
  • Primary Citation of Related Structures:  
    4GCW

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease Z320Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
Gene Names: BSU23840rnzyqjK
EC: 3.1.26.11
UniProt
Find proteins for P54548 (Bacillus subtilis (strain 168))
Explore P54548 
Go to UniProtKB:  P54548
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54548
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
TRNA(THR)76N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.08α = 90
b = 42.55β = 127.18
c = 110.89γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description