BASIL2022GV3R8E

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spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page BASIL2022GV3R8E. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. Abstract The Protein Data Bank (PDB) contains approximately 188 thousand protein structures, 5000 of which have not been assigned a specific function. As a part of the Biochemistry Authentic Scientific Inquiry Laboratory (BASIL) project, we were tasked with analyzing and determining the function of one of these proteins, PDB ID 3r8e. This protein is a putative kinase, which is of interest due to the key roles kinases play in many cellular processes. Utilizing the modules the BASIL consortium provides, a series of in silico and in vitro experiments were conducted. The 3r8e protein was first studied using a variety of in silico tools, including BLASTp, Pfam, and DALI. Based on our in silico results, glucose was determined to be the most likely substrate for 3r8e and was used for further in vitro characterization of the protein. To confirm the in silico function prediction for the 3r8e protein, bacterial protein overexpression, affinity chromatography purification, and coupled kinase activity assays were utilized. Multiple sugar substrates for 3r8e were tested, including glucose. The coupled kinase assay results confirmed that 3r8e likely plays a role in glucose phosphorylation, aligning with our in silico conclusions. Future directions include repeating the above experiments and testing additional hexose substrates to further characterize the enzymatic activity of 3r8e. Overall, we have strong preliminary evidence that the 3r8e protein is a glucose kinase and future work will allow us to confirm this. Introduction Like many proteins with solved crystal structures, protein 3r8e has an uncharacterized and unconfirmed function. Extracted from and being a part of a bacteria that is found in soil, no one knows what the role of this specific protein plays in relation to the bacteria. Apart of a research project, our group set out to solve the function of this protein to then potentially provide further insight of the protein's relationship to the bacteria. Below is the general workflow of how we got our results. Conclusions/Future Direction This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

3. Blastp [Internet]. Bethesda (MD): Natiobal Library of Medicine (US), National Center for Biotechnology Information; 2004- [cited 2022 March]. Available from: (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins)

4. BASIL. https://basilbiochem.github.io/basil/

5. Holm L (2020) Using Dali for protein structure comparison. Methods Mol. Biol. 2112, 29-42.

6. Small- Molecule Library Screening by Docking with PyRx. .Dallakyan S, Olson AJ Methods Mol Biol. 2015;1263:243-50. The full-text is available at https://www.researchgate.net/publications/2739554875. Small-Molecule Library Screening by Docking with PyRx.

7. Pfam: The Protein families database in 2021 J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, R.D. Finn, A. Bateman Nucleic Acids Research (2020) doi: 10.1093/nar/gkaa913

8. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.

Proteopedia Page Contributors and Editors (what is this?)

Michel Evertsen, Dalton Dencklau, Jaime Prilusky, Bonnie Hall