Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.43 kDa 
• Atom Count: 4614 
• Residue Count: 566 
• Unique protein chains: 1

1Y44

Crystal structure of RNase Z

• DOI: 10.2210/pdb1Y44/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-30 Released: 2005-01-25 
• Deposition Author(s): de la Sierra-Gallay, I.L., Pellegrini, O., Condon, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 

Literature

Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.

de la Sierra-Gallay, I.L., Pellegrini, O., Condon, C.

(2005) Nature 433: 657-661

• PubMed: 15654328 
• DOI: 10.1038/nature03284
• Primary Citation of Related Structures:  
  1Y44


• PubMed Abstract: 
  

Transfer RNAs (tRNAs) are synthesized as part of longer primary transcripts that require processing of both their 3' and 5' extremities in every living organism known. The 5' side is processed (matured) by the ubiquitously conserved endonucleolytic ribozyme, RNase P, whereas removal of the 3' tails can be either exonucleolytic or endonucleolytic. The endonucleolytic pathway is catalysed by an enzyme known as RNase Z, or 3' tRNase. RNase Z cleaves precursor tRNAs immediately after the discriminator base (the unpaired nucleotide 3' to the last base pair of the acceptor stem, used as an identity determinant by many aminoacyl-tRNA synthetases) in most cases, yielding a tRNA primed for addition of the CCA motif by nucleotidyl transferase. Here we report the crystal structure of Bacillus subtilis RNase Z at 2.1 A resolution, and propose a mechanism for tRNA recognition and cleavage. The structure explains the allosteric properties of the enzyme, and also sheds light on the mechanisms of inhibition by the CCA motif and long 5' extensions. Finally, it highlights the extraordinary adaptability of the metallo-hydrolase domain of the beta-lactamase family for the hydrolysis of covalent bonds.

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Related Citations: 

• Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis
  Pellegrini, O., Nezzar, J., Marchfelder, A., Putzer, H., Condon, C.
  (2003) EMBO J 22: 4534

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Organizational Affiliation: 

CNRS UPR 9073, Université de Paris 7-Denis Diderot, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease Z	A, B	320	Bacillus subtilis	Mutation(s): 5  Gene Names: rnz EC: 3.1.26.11
Find proteins for P54548 (Bacillus subtilis (strain 168)) Explore P54548  Go to UniProtKB:  P54548

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.98	α = 90
b = 188.33	β = 90
c = 177.91	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-30 
• Released Date: 2005-01-25 
Deposition Author(s): de la Sierra-Gallay, I.L., Pellegrini, O., Condon, C.

Revision History 

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance