BASIL2022GV3HDT

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue. This protein (3HDT) is a putative kinase with possibly cytidylate kinase function utilizing ATP and dCMP as ligands.

Introduction

Kinases (or phosphotransferases) facilitate the transfer of a phosphate group from one molecule to another, and are involved in cell growth and signaling. This work characterizes a protein (PDB ID 3HDT) with unknown function, and tests for kinase activity. In silico tools including BLASTp, Pfam, SPRITE, DALI, DeepFRI, and PyRx were used to hypothesize the function and taxonomy of 3HDT. These results indicated the protein may be a cytidylate kinase (EC: 2.7.4.X) that transfers a phosphate from ATP to dCMP. E. coli. were transformed with a plasmid containing the gene for 3HDT. The protein was then overexpressed, purified and quantified. SDS-PAGE was used to verify the purity of the protein. Kinetics assays were carried out using dCMP as a substrate, showing only limited activity. Future research should focus on other nucleotide substrates such as TMP or GMP, which also showed high affinities in docking simulations.

OR

The goal of this research is to characterize the protein, 3HDT, that has an unknown function. This research is part of the BASIL project that involved performing in silico and in vitro modules to make predictions and study the function of this protein.

In silico anaylsis

We used a variety of in silico tools with our protein, 3HDT to find similarities with other amino acid sequences, protein family matches, and structural comparisons to known proteins in the PDB. Below are the recorded results and information from each database. From this information, a hypothesized function was created for 3HDT and potential substrates were selected such as dCMP.

BLASTp

BLASTp Alignment showing a hit with cytidylate kinase-like family, part of the NK superfamily.

Query hits 1-2 show proteins with unknown function while 3-6 match a cytidylate kinase-like family protein.

Pfam

Pfam results showing cytidylate kinase-like family result.

DALI

Spatial alignment of putative kinase 3HDT (green) with two cytidylate kinases: 7L4A (dark brown) and 1KDO (light brown).

PANZ

Docking

Laboratory Experiments

Coupled kinase assay

Coupled kinase assay diagram (left) with enzymes shown in color and phosphates in yellow. Phosphorylation of dCMP is measured indirectly through the conversion of NADH to NAD+. Background hydrolysis of NADH is measured and subtracted from the conversion rate in the presence of dCMP to produce specific activities (right). 

SDS-PAGE

SDS-PAGE results for the purified protein 3HDT. The total weight of this protein is around 25.79 kD. The first lane (left) contains a size standard. The band in the second lane (right) at ~70kD is not the protein of interest (3HDT) but contains a binding metal protein. There is also a faint band around ~26kD, indicating our protein of interest was present.

Results from running an SDS-PAGE with the purified 3HDT

Conclusion/Future Experiments

Our protein was confirmed to be 3HDT using SDS-PAGE and showed activity during coupled kinase assays. While this confirms that 3HDT is a kinase, the true substrate, however, was likely not dCMP. Further research should be done with molecules such as TMP and GMP in the future to narrow down potential nucleotide substrates or elucidate other types of compounds to be considered as ligands for 3HDT.