Sandbox Reserved 1130
From Proteopedia
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<Structure load='1NZB' size='350' frame='true' align='right' caption='Crystal Structural of wild type Cre recombinase-loxP synapse' /> | <Structure load='1NZB' size='350' frame='true' align='right' caption='Crystal Structural of wild type Cre recombinase-loxP synapse' /> | ||
| - | Cre recombinase is a tyrosine recombinase enzyme<ref>DOI 10.1038/37925</ref> belonging to the integrase family. It catalyses the site-specific recombination between two sequences of DNA called loxP sites. | + | Cre recombinase is a tyrosine recombinase enzyme<ref>DOI 10.1038/37925</ref> belonging to the integrase family of recombinases. 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. | This enzyme was discovered in the P1 bacteriophage and it is now used in research as a means for genome editing. | ||
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==Structure == | ==Structure == | ||
| - | The Cre | + | The Cre recombinase protein contains 343 amino acids and the mass of this proteins is 38,540 Dalton. |
| - | There are two different important | + | There are two different important domains : |
| - | 10-125 : amino terminal domain = SAM domain like (steril alpha motif) <ref>DOI 10.1016/j.tibs.2003.11.001</ref>. It | + | 10-125 : amino terminal domain = SAM domain like (steril alpha motif) <ref>DOI 10.1016/j.tibs.2003.11.001</ref>. It is corresponding of a 4-5 helices : bundle of two orthogonally packed alpha-hairpins. It involved too in the interactions with DNA and proteins. The amino termain domain contains 5 helix. |
| - | The other domain is the carboxy terminal domain (130-343). It contains helices and | + | The other domain is the carboxy terminal domain (130-343). It contains helices and beta sheets. |
| - | The helical in Cre-recombinase | + | The helical parts in Cre-recombinase represent 52% and the Beta sheets parts represent only 5% of the secondary structure of the protein. |
| - | This proteins is composed of a | + | This proteins is composed of a catalytic triade (Arg 173, His 289, Arg 292) and interacts with magnesium. |
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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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1NZB Cre recombinase-loxP synapse
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Cre recombinase is a tyrosine recombinase enzyme[1] belonging to the integrase family of recombinases. 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.
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.
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.
Sequence used to form Cre/DNA cocrystal loxP[4]
5' -ATAACTTCGTATAGCATACATTATACGAAGTTAT 3'
3' -TATTGAAGCATATCGTATGTAATATGCTTCAATA 5'
DNA Substrate
5' -TATAACTTCGTATAGCATATGCTATACGAAGTTAT- 3'
3' -TATTGAAGCATATCGTATACGATATGCTTCAATA- 5'
Structure
The Cre recombinase protein contains 343 amino acids and the mass of this proteins is 38,540 Dalton. There are two different important domains : 10-125 : amino terminal domain = SAM domain like (steril alpha motif) [5]. It is corresponding of a 4-5 helices : bundle of two orthogonally packed alpha-hairpins. It involved too in the interactions with DNA and proteins. The amino termain domain contains 5 helix.
The other domain is the carboxy terminal domain (130-343). It contains helices and beta sheets. The helical parts in Cre-recombinase represent 52% and the Beta sheets parts represent only 5% of the secondary structure of the protein. This proteins is composed of a catalytic triade (Arg 173, His 289, Arg 292) and interacts with magnesium.
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.
</StructureSection>
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ Kim CA, Bowie JU. SAM domains: uniform structure, diversity of function. Trends Biochem Sci. 2003 Dec;28(12):625-8. PMID:14659692 doi:http://dx.doi.org/10.1016/j.tibs.2003.11.001
