6MYX

EM structure of Bacillus subtilis ribonucleotide reductase inhibited double-helical filament of NrdE alpha subunit with dATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Convergent allostery in ribonucleotide reductase.

Thomas, W.C.Brooks 3rd, F.P.Burnim, A.A.Bacik, J.P.Stubbe, J.Kaelber, J.T.Chen, J.Z.Ando, N.

(2019) Nat Commun 10: 2653-2653

  • DOI: 10.1038/s41467-019-10568-4
  • Primary Citation of Related Structures:  
    6MT9, 6MV9, 6MVE, 6MW3, 6MYX

  • PubMed Abstract: 
  • Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity ...

    Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA. nozomi.ando@cornell.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductaseA [auth C],
B [auth D],
C [auth I],
D [auth J]
700Bacillus subtilisMutation(s): 0 
Gene Names: nrdE_1B4417_3413NCTC3610_03984
EC: 1.17.4.1
UniProt
Find proteins for P50620 (Bacillus subtilis (strain 168))
Explore P50620 
Go to UniProtKB:  P50620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50620
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100008

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence