5F6C | pdb_00005f6c

The structure of E. coli RNase E catalytically inactive mutant with RNA bound

PDB DOI: https://doi.org/10.2210/pdb5F6C/pdb
NAKB: 5F6C

Classification: HYDROLASE
Organism(s): Escherichia coli K-12, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-12-05 Released: 2016-12-14
Deposition Author(s): Bandyra, K.J., Luisi, B.F.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.250 (Depositor), 0.248 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.molcel.2018.08.039
Primary Citation 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: kjb69@cam.ac.uk.

Macromolecule Content

Total Structure Weight: 117.32 kDa
Atom Count: 8,088
Modeled Residue Count: 1,027
Deposited Residue Count: 1,030
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	A	512	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21513
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease E	B	513	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21513
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
RNA (5'-R(PGPU)-3')	C	2	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
RNA (5'-R(PGPUP*G)-3')	D [auth E]	3	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.250 (Depositor), 0.248 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.619	α = 90
b = 122.562	β = 99.77
c = 122.195	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Bandyra, K.J.

Luisi, B.F.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	076846/Z/05/A

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release
Version 1.1: 2018-10-10
Changes: Data collection, Database references, Structure summary
Version 1.2: 2019-02-27
Changes: Data collection, Database references, Structure summary
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations