Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 247.05 kDa 
• Atom Count: 16901 
• Residue Count: 2174 
• Unique protein chains: 1

3ZQ4

Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1

• DOI: 10.2210/pdb3ZQ4/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-06-07 Released: 2011-09-14 
• Deposition Author(s): Newman, J.A., Hewitt, L., Rodrigues, C., Solovyova, A., Harwood, C.R., Lewis, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of Rnase J1.

Newman, J.A., Hewitt, L., Rodrigues, C., Solovyova, A., Harwood, C.R., Lewis, R.J.

(2011) Structure 19: 1241

• PubMed: 21893285 
• DOI: 10.1016/j.str.2011.06.017
• Primary Citation of Related Structures:  
  3ZQ4


• PubMed Abstract: 
  

RNase J is an essential enzyme in Bacillus subtilis with unusual dual endonuclease and 5'-to-3' exonuclease activities that play an important role in the maturation and degradation of mRNA. RNase J is also a component of the recently identified "degradosome" of B. subtilis. We report the crystal structure of RNase J1 from B. subtilis to 3.0 Å resolution, analysis of which reveals it to be in an open conformation suitable for binding substrate RNA. RNase J is a member of the β-CASP family of zinc-dependent metallo-β-lactamases. We have exploited this similarity in constructing a model for an RNase J1:RNA complex. Analysis of this model reveals candidate-stacking interactions with conserved aromatic side chains, providing a molecular basis for the observed enzyme activity. Comparisons of the B. subtilis RNase J structure with related enzymes reveal key differences that provide insights into conformational changes during catalysis and the role of the C-terminal domain.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE J 1	A, C, D, E	555	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: rnjA, ykqC, BSU14530 EC: 3.1
Find proteins for Q45493 (Bacillus subtilis (strain 168)) Explore Q45493  Go to UniProtKB:  Q45493

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, C, D, E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, C, D, E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.823	α = 90
b = 209.43	β = 90
c = 74.106	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-07 
• Released Date: 2011-09-14 
Deposition Author(s): Newman, J.A., Hewitt, L., Rodrigues, C., Solovyova, A., Harwood, C.R., Lewis, R.J.

Revision History 

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-07-10
  Changes: Data collection