Sandbox Reserved 1130

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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.

To get started: Click the edit this page tab at the top. Save the page after each step, then edit it again. Click the 3D button (when editing, above the wikitext box) to insert Jmol. show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page. Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc. More help: Help:Editing

1NZB Cre recombinase-loxP synapse

spinqualitylabelsall models Crystal Structural of wild type Cre recombinase-loxP synapse Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Cre recombinase is a tyrosine recombinase enzyme^[1] belonging to the integrase family. It catalyses the site-specific recombination between two sequences of DNA called loxP sites. This enzyme was discovered in the P1 bacteriophage and it is now used in research as a means for genome editing in mammalian cells and plants.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[2] or to the article describing Jmol ^[3] to the rescue.

Contents 1 Function 2 Structure 2.1 Primary structure 2.2 Secondary structure 2.3 Tertiary structure 2.3.1 Active site 2.4 Quaternary structure 3 References

Function

Reference : Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation. ^[4]

Sequence used to form Cre/DNA cocrystal loxP

5' -ATAACTTCGTATAGCATACATTATACGAAGTTAT 3'

3' -TATTGAAGCATATCGTATGTAATATGCTTCAATA 5'

DNA Substrate

5' -TATAACTTCGTATAGCATATGCTATACGAAGTTAT- 3'

3' -TATTGAAGCATATCGTATACGATATGCTTCAATA- 5'

Structure

Primary structure

The Cre-recombinase protein contains 343 aa and the mass of this proteins is 38,540 Dalton.

There are two different important domain.

10-125 : amino terminal domain

130 - 343 : carboxy terminal domain

Secondary structure

The amino terminal domain contains 5 helix. The carboxy terminal domain contains helix and sheets.

Tertiary structure

Active site

This proteins is composed of a triade catalytic residues (Arg 173, His 289, Arg 292)

Quaternary structure

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. ↑ Guo F, Gopaul DN, van Duyne GD. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 1997 Sep 4;389(6646):40-6. PMID:9288963 doi:10.1038/37925
2. ↑ 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
3. ↑ 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
4. ↑ Ennifar E, Meyer JE, Buchholz F, Stewart AF, Suck D. Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation. Nucleic Acids Res. 2003 Sep 15;31(18):5449-60. PMID:12954782