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Crystal Structure of the Brugia malayi Thymidylate Kinase-dTMP Complex and Small Angle X-ray Scattering Experiments Identifies Changes in the Dimeric Association Compared to the Human Homolog

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Abstract—

Lymphatic filariasis is a serious parasitic disease spread by mosquitoes and affects the lymphatic system resulting in abnormal enlargement of body parts. It is caused by three related nematodes, one of which is Brugia malayi. Thymidylate kinase (TMK) is the principal enzyme involved in nucleic acid metabolism. It synthesizes pyrimidine by catalyzing the phosphorylation of thymidine-5'-monophosphate (dTMP) to form thymidine-5'-diphosphate (dTDP) in the presence of Mg2+ and ATP. Hence TMK could be an attractive drug target to develop new anti-filarials. Here, we report the crystal structure of dTMP substrate bound Brugia malayi thymidylate kinase (BmTMK) to 1.91 Å resolution. The structure adopts the classic α/β fold like P-loop NTPases with core and Nucleotide binding domains. A comparison with the human homolog shows several differences in the TMK binding site and also in the dimeric association. Small-angle X-ray scattering (SAXS) experiments support the differences in the dimeric association between BmTMK and its human counterpart. The differences in the active site architecture can possibly be exploited to develop BmTMK specific inhibitors.

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ACKNOWLEDGMENTS

Brugia malayi thymidylate kinase cloned in pET28a expression vector was received as a kind gift from Dr. Saxena, CSIR-Central Drug Research Institute, Lucknow.

Funding

The project was supported by a grant from Council of Scientific and Industrial Research, India with no. BSC0104. The manuscript has a CSIR-CDRI communication no. 141/2021/RR.

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Authors and Affiliations

  1. CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India

    J. Vishwakarma, V. K. Sharma, S. Kumar & R. Ramachandran

  2. Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India

    J. Vishwakarma, S. Kumar & R. Ramachandran

Authors
  1. J. Vishwakarma
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  2. V. K. Sharma
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  3. S. Kumar
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  4. R. Ramachandran
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Correspondence to J. Vishwakarma, V. K. Sharma or R. Ramachandran.

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CONFLICT OF INTEREST

The authors of this work declare that they have no conflicts of interest.

DATA SUBMISSION

The SAXS generated data was submitted to SASBDB as SASDKU9 while crystals structure coordinates were submitted to the Protein data bank with PDB ID: 7FGQ.

Original amino acids sequence of BmTMK MGSRIRGAFIVFEGCDRAGKSLQSRKLVERIKAAGGDVDLISFPDRSSDLGKFIDRYLKKEVEMDPKEAHLVFAANRQALMPLMMKKLLKGTHLVVDRYAYSGIAYTLAKGADNITMEWAKLADMGELRPDCVIYFNLSFEEAQKRSGFGDERFDFGNFQGKVSKVMEQLADEDRDLWKVVDASLTVEEISENVWNLVAPILDNVSRKSL.

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Vishwakarma, J., Sharma, V.K., Kumar, S. et al. Crystal Structure of the Brugia malayi Thymidylate Kinase-dTMP Complex and Small Angle X-ray Scattering Experiments Identifies Changes in the Dimeric Association Compared to the Human Homolog. Crystallogr. Rep. 68, 1150–1158 (2023). https://doi.org/10.1134/S1063774521100400

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