6CQI

2.42A Crystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with an oligonucleotide MTS2-11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.

Cao, N.Tan, K.Annamalai, T.Joachimiak, A.Tse-Dinh, Y.C.

(2018) Nucleic Acids Res 46: 7296-7308

  • DOI: 10.1093/nar/gky492
  • Primary Citation of Related Structures:  
    6CQ2, 5UJY, 6CQI, 5UJ1

  • PubMed Abstract: 
  • We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage ...

    We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.


    Organizational Affiliation

    Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 1A706Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: topARv3646cMTCY15C10.06
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P9WG49 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG49 
Go to UniProtKB:  P9WG49
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3')B11Mycobacterium tuberculosis
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    E [auth A]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    ACT
    Query on ACT

    Download Ideal Coordinates CCD File 
    F [auth A], G [auth A], H [auth A]ACETATE ION
    C2 H3 O2
    QTBSBXVTEAMEQO-UHFFFAOYSA-M
     Ligand Interaction
    FMT
    Query on FMT

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A]FORMIC ACID
    C H2 O2
    BDAGIHXWWSANSR-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.42 Å
    • R-Value Free: 0.269 
    • R-Value Work: 0.224 
    • R-Value Observed: 0.226 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 68.777α = 90
    b = 44.977β = 90.6
    c = 129.229γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    HKL-3000phasing

    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 StatesGM054226
    Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
    TB AllianceUnited States--

    Revision History  (Full details and data files)

    • Version 1.0: 2018-05-30
      Type: Initial release
    • Version 1.1: 2018-07-04
      Changes: Data collection, Database references
    • Version 1.2: 2018-09-05
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-04
      Changes: Author supporting evidence