4WOP

Nucleotide Triphosphate Promiscuity in Mycobacterium tuberculosis Dethiobiotin Synthetase

Summary for 4WOP

• Entry DOI: 10.2210/pdb4wop/pdb
• Descriptor: ATP-dependent dethiobiotin synthetase BioD, CYTIDINE-5'-TRIPHOSPHATE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: biotin protein ligase, ligase
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm : A5U2S7
• Total number of polymer chains: 4
• Total formula weight: 91356.60

Authors

Salaemae, W.,Yap, M.Y.,Wegener, K.L.,Booker, G.W.,Wilce, M.C.J.,Polyak, S.W. (deposition date: 2014-10-16, release date: 2015-04-08, Last modification date: 2023-12-27)

Primary citation

Salaemae, W.,Yap, M.Y.,Wegener, K.L.,Booker, G.W.,Wilce, M.C.,Polyak, S.W.
Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase.
Tuberculosis (Edinb), 95:259-266, 2015

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.

PubMed: 25801336
DOI: 10.1016/j.tube.2015.02.046

Experimental method

X-RAY DIFFRACTION (2.393 Å)