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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.
Function of your protein
You can see the two-part portion of the protein. The protein has been made somewhat transparent so you can see the substrate within the ligand.
The Chorismate Dehydratatase MqnA is an enzyme that acts upon chorismate, a biochemical intermediate in plants and microorganisms. On the futalosine pathway, it converts chorismate to EPB by removing water. MqnA is the only known chorismate dehydratase.
The futalosine pathway biosynthesizes menaquinone, a carrier of electrons in electron transport chain in prokaryotes. Menaquinone is important for a number of functions in the human body, including cell growth control, apoptosis, and the metabolism of calcium, to name a few. As the human body cannot create menaquinone, it derives it from intestinal bacteria, diet, or by converting plant vitamin K1 (phylloquinone).
The example we are showing is from Streptomyces coelicolor. The other mutant MqnA are from Escherichia coli.
The substrate for MqnA is chorismate. It is converted to menaquinone through two different pathways, the futalosine or the o-succinyl-benzoate pathways. On the futalosine pathway, chorismate is converted to 3-enolpyruvyl-benzoate (3-EPB) by our enzyme of interest.
Biological relevance and broader implications
Important amino acids
These are the important amino acids within the ligand.
Structural highlights
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.
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:https://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644