2BX2

Catalytic domain of E. coli RNase E

• PDB DOI:  https://doi.org/10.2210/pdb2BX2/pdb
• NAKB: 2BX2

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-07-21 Released: 2005-10-14 
• Deposition Author(s): Marcaida, M.J., Callaghan, A.J., Scott, W.G., Luisi, B.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.257 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 

Literature

Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover

Callaghan, A.J., Marcaida, M.J., Stead, J.A., Mcdowall, K.J., Scott, W.G., Luisi, B.F.

(2005) Nature 437: 1187

• PubMed: 16237448 
• DOI: https://doi.org/10.1038/nature04084
• Primary Citation of Related Structures:  
  2BX2, 2C0B, 2C4R


• PubMed Abstract: 
  

The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors. RNase E cleaves RNA internally, but its catalytic power is determined by the 5' terminus of the substrate, even if this lies at a distance from the cutting site. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5' terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.

---

Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.02 kDa 
• Atom Count: 4,135 
• Modelled Residue Count: 514 
• Deposited Residue Count: 532 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE E	A [auth L]	517	Escherichia coli	Mutation(s): 0  EC: 3.1.4 (PDB Primary Data), 3.1.26.12 (UniProt)
UniProt
Find proteins for P21513 (Escherichia coli (strain K12)) Explore P21513  Go to UniProtKB:  P21513

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP* UP*GP*UP*U)-3')	B [auth R]	15	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth L], D [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.257 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.838	α = 90
b = 195.838	β = 90
c = 143.569	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-14 
Deposition Author(s): Marcaida, M.J., Callaghan, A.J., Scott, W.G., Luisi, B.F.

Revision History  

• Version 1.0: 2005-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance