6JMI | pdb_00006jmi

Crystal structure of M.tuberculosis Rv0081

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.301 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.265 (Depositor) 

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Literature

Structural basis of hypoxic gene regulation by the Rv0081 transcription factor of Mycobacterium tuberculosis.

Kumar, A., Phulera, S., Rizvi, A., Sonawane, P.J., Panwar, H.S., Banerjee, S., Sahu, A., Mande, S.C.

(2019) FEBS Lett 593: 982-995

  • DOI: https://doi.org/10.1002/1873-3468.13375
  • Primary Citation of Related Structures:  
    6JMI

  • PubMed Abstract: 

    The transcription factor Rv0081 of Mycobacterium tuberculosis controls hypoxic gene expression and acts as a regulatory hub in the latent phase of tuberculosis (TB) infection. We report here the crystal structure of Rv0081 at 2.9 Å resolution revealing that it belongs to the well-known ArsR/SmtB family proteins. However, unlike other members in this family, Rv0081 has neither a metal-binding domain nor does it possess Cys residues, suggesting an alternate mechanism of gene regulation. Our structural and biochemical analyses suggest the molecular basis for the recognition of self-regulatory DNA sequences and a plausible mechanism of regulation of Rv0081 in the latent phase of TB infection. DATABASE: Structural data are available in the Protein Data Bank under the accession number - 6JMI.

    • Organizational Affiliation: 
    • National Centre for Cell Science, SP Pune University Campus, Pune, India.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized HTH-type transcriptional regulator Rv0081
A, B, C, D
114Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0081
UniProt
Find proteins for P9WMI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMI7 
Go to UniProtKB:  P9WMI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.301 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.265 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.317α = 90
b = 63.317β = 90
c = 262.604γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Biotechnology (India)IndiaBT/PR3260/BRB/10/967/2011
Department of Biotechnology (India)IndiaBT/PR15450/COE/34/46/2016

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references
  • Version 1.4: 2025-03-12
    Changes: Database references, Structure summary