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Introduction

Hey guys you can use this link for more info about TMK. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242479/ ^[1] This is a sample scene created with SAT to by Group, and another to make of the protein.

Overall Structure

Thymidylate Kinase has clearly defined secondary and tertiary structures. The consists of 5 beta sheets and 8 alpha helices. The Sulfonylpiperidine ligand is shown as a surface in this representation as the ligand is not particularly relevant to the secondary structure. The beta sheets and alpha helices are connected by turns, or chains of amino acids, shown in black. Additionally, it is good to note that for Thymidylate Kinase, beta sheets are arranged in an parallel fashion using short turns and alpha helices to connect. Coloring from red to blue from the , it is clear the Thymidylate Kinase consists of two clear mirrored units with each unit binding a Sulfonylpiperidine ligand. The polarity of amino acid units in the beta sheets and alpha helices is a large factor which determined the tertiary structure of this protein. residues are shown in purple, whereas nonpolar are shown in gray. As you can see, the parts of the alpha helices and beta sheets that make up the surface contact are polar, whereas the hydrophobic core of the protein contains the hydrophobic, nonpolar parts of the helices and sheets.

Binding Interactions

Green scene gives a rough outline of the TMK backbone and a look at its active site. Outlined, in ball and stick model, are the active site residues as well as the bound sulfonylpiperidine ligand. The key residues are Arg 48, Phe 66, Ser 97, and Gln 101. In green scene you are able to see that Arg 48, Ser 97, and Gln 101 form hydrogen bonds with the sulfonylpiperidine ligand. The hydrogen bond locations are shown with distances between the atoms which hydrogen bond with each other in one of the subunits. Arg 48 in particular forms one hydrogen bond with the phenolic group on the ligand. The ligand's ability to hydrogen bond with this particular residue was crucial because Arg 48 is a highly conserved residue. In other words it is seen in the active site in other TMK organisms. Moreover the hydrogen bond with Arg 48 is necessary in order for the ligand to have high enzyme affinity. If this sulfonylpiperidine is able to hydrogen bond with Arg 48, it will also be able to have relatively high binding affinity to the TMK of other oganisms. Will edit as other sections are added. ^[2]

Additional Features

Substrate Binding:

• Green scene of TMP-binding site in TMK*

-Conserved throughout all TMKs:

--P-loop carboxylic residue Glu 11 with 3'-OH of TMP

--aromatic ring stacking interactions (pyrimidine ring with phenylalanine (Phe 66) side chain

--Tyr 100 positioning (deoxynucleotide specific)

--h-bond between O4 of pyrimidine moeity with the side chain of Arg 70 (T specific)

• Green Scene highlights these areas of the molecule*

Quiz Question 1

Quiz Question 2

See Also

• 4hld
• Thymidylate_kinase

Credits

Introduction - name of team member

Overall Structure - Jeremy Gilbride

Drug Binding Site - Ross Furash

Additional Features - Randy Phan/Laura Ornes

Quiz Question 1 - Laura Ornes

Quiz Question 2 - name of team member

References

1. ↑ Kotaka M, Dhaliwal B, Ren J, Nichols CE, Angell R, Lockyer M, Hawkins AR, Stammers DK. Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding. Protein Sci. 2006 Apr;15(4):774-84. Epub 2006 Mar 7. PMID:16522804 doi:10.1110/ps.052002406
2. ↑ Martinez-Botella G, Loch JT, Green OM, Kawatkar SP, Olivier NB, Boriack-Sjodin PA, Keating TA. Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK). Bioorg Med Chem Lett. 2013 Jan 1;23(1):169-73. doi: 10.1016/j.bmcl.2012.10.128., Epub 2012 Nov 5. PMID:23206863 doi:http://dx.doi.org/10.1016/j.bmcl.2012.10.128