6BS8

The class 3 DnaB intein from Mycobacterium smegmatis

  • Classification: HYDROLASE
  • Organism(s): Mycolicibacterium smegmatis
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-12-01 Released: 2018-11-21 
  • Deposition Author(s): Li, Z., Kelley, D.S., Banavali, N., Belfort, M., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mycobacterial DnaB helicase intein as oxidative stress sensor.

Kelley, D.S.Lennon, C.W.Li, Z.Miller, M.R.Banavali, N.K.Li, H.Belfort, M.

(2018) Nat Commun 9: 4363-4363

  • DOI: https://doi.org/10.1038/s41467-018-06554-x
  • Primary Citation of Related Structures:  
    6BS8

  • PubMed Abstract: 

    Inteins are widespread self-splicing protein elements emerging as potential post-translational environmental sensors. Here, we describe two inteins within one protein, the Mycobacterium smegmatis replicative helicase DnaB. These inteins, DnaBi1 and DnaBi2, have homology to inteins in pathogens, splice with vastly varied rates, and are differentially responsive to environmental stressors. Whereas DnaBi1 splicing is reversibly inhibited by oxidative and nitrosative insults, DnaBi2 is not. Using a reporter that measures splicing in a native intein-containing organism and western blotting, we show that H 2 O 2 inhibits DnaBi1 splicing in M. smegmatis. Intriguingly, upon oxidation, the catalytic cysteine of DnaBi1 forms an intramolecular disulfide bond. We report a crystal structure of the class 3 DnaBi1 intein at 1.95 Å, supporting our findings and providing insight into this splicing mechanism. We propose that this cysteine toggle allows DnaBi1 to sense stress, pausing replication to maintain genome integrity, and then allowing splicing immediately when permissive conditions return.


  • Organizational Affiliation

    Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, 12222, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicative DNA helicase
A, B, C
139Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: dnaBERS451418_06678
EC: 3.6.4.12
UniProt
Find proteins for I7FPC4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7FPC4 
Go to UniProtKB:  I7FPC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7FPC4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.05α = 90
b = 56.914β = 106.6
c = 64.727γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesGM39422
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM44844
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI055429
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103393
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Refinement description