5YDC

Crystal structure of mercury soaked C-terminal domain of Rv1828 from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characteristics of the essential pathogenicity factor Rv1828, a MerR family transcription regulator from Mycobacterium tuberculosis.

Singh, S.Sevalkar, R.R.Sarkar, D.Karthikeyan, S.

(2018) FEBS J 285: 4424-4444

  • DOI: https://doi.org/10.1111/febs.14676
  • Primary Citation of Related Structures:  
    5YDC, 5YDD

  • PubMed Abstract: 

    The gene Rv1828 in Mycobacterium tuberculosis is shown to be essential for the pathogen and encodes for an uncharacterized protein. In this study, we have carried out biochemical and structural characterization of Rv1828 at the molecular level to understand its mechanism of action. The Rv1828 is annotated as helix-turn-helix (HTH)-type MerR family transcription regulator based on its N-terminal amino acid sequence similarity. The MerR family protein binds to a specific DNA sequence in the spacer region between -35 and -10 elements of a promoter through its N-terminal domain (NTD) and acts as transcriptional repressor or activator depending on the absence or presence of effector that binds to its C-terminal domain (CTD). A characteristic feature of MerR family protein is its ability to bind to 19 ± 1 bp DNA sequence in the spacer region between -35 and -10 elements which is otherwise a suboptimal length for transcription initiation by RNA polymerase. Here, we show the Rv1828 through its NTD binds to a specific DNA sequence that exists on its own as well as in other promoter regions. Moreover, the crystal structure of CTD of Rv1828, determined by single-wavelength anomalous diffraction method, reveals a distinctive dimerization. The biochemical and structural analysis reveals that Rv1828 specifically binds to an everted repeat through its winged-HTH motif. Taken together, we demonstrate that the Rv1828 encodes for a MerR family transcription regulator.


  • Organizational Affiliation

    CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized HTH-type transcriptional regulator Rv1828
A, B
142Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1828MTCY1A11.15c
UniProt
Find proteins for P9WME7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WME7 
Go to UniProtKB:  P9WME7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WME7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.355α = 90
b = 31.511β = 98.21
c = 77.901γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CSIR-INSTITUTE OF MICROBIAL TECHNOLOGYIndiaBSC0210, BSC0104

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations