6G63

RNase E in complex with sRNA RrpA

• PDB DOI: https://doi.org/10.2210/pdb6G63/pdb
• NAKB: 6G63

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli K-12, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-31 Released: 2018-10-03 
• Deposition Author(s): Bandyra, K.B., Luisi, B.F.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free: 0.296 
• R-Value Work: 0.275 
• R-Value Observed: 0.276 

Literature

Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E.

Bandyra, K.J., Wandzik, J.M., Luisi, B.F.

(2018) Mol Cell 72: 275-285.e4

• PubMed: 30270108 
• DOI: https://doi.org/10.1016/j.molcel.2018.08.039
• Primary Citation of Related Structures:  
  5F6C, 6G63


• PubMed Abstract: 
  

  The endoribonuclease RNase E is a principal factor in RNA turnover and processing that helps to exercise fine control of gene expression in bacteria. While its catalytic activity can be strongly influenced by the chemical identity of the 5' end of RNA substrates, the enzyme can also cleave numerous substrates irrespective of the chemistry of their 5' ends through a mechanism that has remained largely unexplained. We report structural and functional data illuminating details of both operational modes. Our crystal structure of RNase E in complex with the sRNA RprA reveals a duplex recognition site that saddles an inter-protomer surface to help present substrates for cleavage. Our data also reveal an autoinhibitory pocket that modulates the overall activity of the ribonuclease. Taking these findings together, we propose how RNase E uses versatile modes of RNA recognition to achieve optimal activity and specificity.

---

Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 238.49 kDa 
• Atom Count: 16,148 
• Modelled Residue Count: 1,997 
• Deposited Residue Count: 2,067 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	A, B [auth G], C [auth L], D [auth N]	510	Escherichia coli K-12	Mutation(s): 2  Gene Names: rne, ams, hmp1, b1084, JW1071 EC: 3.1.26.12
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(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')	E [auth B]	27	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U	H [auth N]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
ZN	F [auth A], G [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free: 0.296 
• R-Value Work: 0.275 
• R-Value Observed: 0.276 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.63	α = 90
b = 110.63	β = 90
c = 466.02	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Bandyra, K.B., Luisi, B.F.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	200873/Z/16/Z

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-10-31
  Changes: Data collection, Database references, Structure summary