7F70

Crystal structure of Rv3094c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene.

Wan, L.Hu, P.Zhang, L.Wang, Z.X.Fleming, J.Ni, B.Luo, J.Guan, C.X.Bai, L.Tan, Y.Liu, H.Li, N.Xiao, T.Bai, H.Zhang, Y.A.Zhang, X.E.Wan, K.Bi, L.Ouyang, S.Zhang, H.

(2023) Commun Biol 6: 156-156

  • DOI: https://doi.org/10.1038/s42003-023-04433-w
  • Primary Citation of Related Structures:  
    7F70, 7F72, 7F74

  • PubMed Abstract: 

    Global control of the tuberculosis epidemic is threatened by increasing prevalence of drug resistant M. tuberculosis isolates. Many genome-wide studies focus on SNP-associated drug resistance mechanisms, but drug resistance in 5-30% of M. tuberculosis isolates (varying with antibiotic) appears unrelated to reported SNPs, and alternative drug resistance mechanisms involving variation in gene/protein expression are not well-studied. Here, using an omics approach, we identify 388 genes with lineage-related differential expression and 68 candidate drug resistance-associated gene pairs/clusters in 11 M. tuberculosis isolates (variable lineage/drug resistance profiles). Structural, mutagenesis, biochemical and bioinformatic studies on Rv3094c from the Rv3093c-Rv3095 gene cluster, a gene cluster selected for further investigation as it contains a putative monooxygenase/repressor pair and is associated with ethionamide resistance, provide insights on its involvement in ethionamide sulfoxidation, the initial step in its activation. Analysis of the structure of Rv3094c and its complex with ethionamide and flavin mononucleotide, to the best of our knowledge the first structures of an enzyme involved in ethionamide activation, identify key residues in the flavin mononucleotide and ethionamide binding pockets of Rv3094c, and F221, a gate between flavin mononucleotide and ethionamide allowing their interaction to complete the sulfoxidation reaction. Our work broadens understanding of both lineage- and drug resistance-associated gene/protein expression perturbations and identifies another player in mycobacterial ethionamide metabolism.


  • Organizational Affiliation

    Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rv3094c376Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv3094c
UniProt
Find proteins for O05773 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O05773 
Go to UniProtKB:  O05773
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05773
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.322α = 90
b = 134.322β = 90
c = 110.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB29020000
National Science Foundation (NSF, China)China2018ZX10101004
National Natural Science Foundation of China (NSFC)China31770148
National Natural Science Foundation of China (NSFC)China31770150
National Natural Science Foundation of China (NSFC)China31770948
National Natural Science Foundation of China (NSFC)China31570875

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description