Sandbox Reserved 1132

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This Sandbox is Reserved from 15/12/2015, through 15/06/2016 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1120 through Sandbox Reserved 1159.
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Contents

Your Heading Here (maybe something like 'Structure')

This is a default text for your page '. 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 [1] or to the article describing Jmol [2] to the rescue.

Structure

FPPS is a dimer made of two identical subunits, which each contain 13 ά-helices and connecting loops. The regions which connect the helices ά4-ά5 and ά8-ά9 are extended. Within the handle of helices FPPS has a large central cavity, which acts as a hydrophobic ligand-binding site. The site-chain of Phe-113 limits the cavity on one site. The helices ά4 and ά8 contain highly conserved and aspartate-rich motives (103DDIUD107 and 243DDYLD247). A distinctive kink in helix ά7 turns carbonyl of Lys-200 in the direction of the cavity.

Biological Function

  • Interactions
    • Interactions with N-BP

The side chain is located in the hydrophobic cleft that normally accomodates an isoprenoid lipid, and the phosphonate groups are bound to a cluster of three Mg2+ ions, which were chelated by two asparate-rich motifs.

There is a large cavity in the helical bundle that forms a partly hydrophobic ligand-binding site. This cavity is delimited by Phe-113.

N-BP binding causes a structural rearrangement and a decrease of size in the internal cavity. The movement is mediated by ά4 and ά8 which participate in the ligand binding. Many connections occur in this movement : residues 249-268 bind over the N-BP and stay in place because of polar interactions : loop residue Lys-257 contacts Asp-243 and a phosphonate oxygen. Asp-247 at the end of a8 forms bidentate hydrogen bonds with main-chain amides of Thr-260 and Asp-261. The main chain from Ile-258 to Thr-260 is separated. The heterocyclic ring structures of RIS and ZOL are sur- rounded mainly by hydrophobic side chains of residues Phe-99, Leu-100, Thr-167, Lys-200, and Tyr-204, and the nitrogen atom of the ring system is found within hydrogen-bonding. There is a network of salt links involving Lys-57, the terminal carboxylate of Lys-353, and Arg-351.


  • Pathway
  • Diseases

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

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References

  1. ↑ 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:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ 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
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