4WOP

Nucleotide Triphosphate Promiscuity in Mycobacterium tuberculosis Dethiobiotin Synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase.

Salaemae, W.Yap, M.Y.Wegener, K.L.Booker, G.W.Wilce, M.C.Polyak, S.W.

(2015) Tuberculosis (Edinb) 95: 259-266

  • DOI: https://doi.org/10.1016/j.tube.2015.02.046
  • Primary Citation of Related Structures:  
    4WOP

  • PubMed Abstract: 

    Dethiobiotin synthetase (DTBS) plays a crucial role in biotin biosynthesis in microorganisms, fungi, and plants. Due to its importance in bacterial pathogenesis, and the absence of a human homologue, DTBS is a promising target for the development of new antibacterials desperately needed to combat antibiotic resistance. Here we report the first X-ray structure of DTBS from Mycobacterium tuberculosis (MtDTBS) bound to a nucleotide triphosphate (CTP). The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. This resulted in the unexpected finding that MtDTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values, although the enzyme had the highest affinity for CTP in competitive binding and surface plasmon resonance assays. This is in contrast to other DTBS homologues that preferentially bind ATP primarily through hydrogen-bonds between the purine base and the carboxamide side chain of a key asparagine. Mutational analysis performed alongside in silico experiments revealed a gate-keeper role for Asn175 in Escherichia coli DTBS that excludes binding of other nucleotide triphosphates. Here we provide evidence to show that MtDTBS has a broad nucleotide specificity due to the absence of the gate-keeper residue.


  • Organizational Affiliation

    School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent dethiobiotin synthetase BioD
A, B, C, D
225Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: bioDMRA_1582
EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPQ5 
Go to UniProtKB:  P9WPQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPQ5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.56α = 90
b = 104.33β = 90
c = 152.34γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Structure summary
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy