User:Brian Ochoa/Sandbox 1

From Proteopedia

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This is a default text for your page Brian Ochoa/Sandbox 1. 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.

Structural Highlights

BRCA1 is an 1,863 amino acid long protein that contains a ring finger motif from position 24 to 64. The ring motif is part of a larger domain spanning the first one hundred amino acid residues, which is required for the formation of its stable structure. This N-terminus domain is of the most highly conserved region of the BRCA1 gene and several cancer-predisposition mutations have been identified in this region.^[3] The ring motif is also a , named so for the conserved pattern of cysteine and histidines residues that bind the zinc ions.^[4] Ultimately, the ring motif of forms a heterodimer with the ring motif of to assemble the functional protein complex. The solution structure of this complex shows that long alpha helices border the zinc binding residues in the ring motif. These alpha helices from the ring motif’s of BRCA1 and BARD1 combine to form a that stabilizes the heterodimer and positions the zinc binding regions next to one another. ^[5]

As highlighted by Dr. Berndsen in his review, the mechanism by which the RING domain facilitates the transfer of the ubiquitin from the E2 to the target protein is largely by allosteric means. The heterodimer of BRCA1-BARD1 is believed to position the donor ubiquitin on the E2 protein in the active site so that the thioester bond between the E2 and the C-terminus of the donor ubiquitin can be easily attacked by the lysine. Correct positioning of this bond by the RING domain thus helps increase the reaction rate of hydrolysis of the thioester. Other conserved residues in the active site have been proposed to facilitate ubiquitination such as acidic residues which may deprotonate, and thus activate the attacking lysine. Additionally, a conserved asparagine has been suggested to be important to either stabilize the oxyanion intermediate or maintain the correct orientation of active site residues. ^[6]

Functional Highlights

One main function of the ring finger domain of BRCA1 is to mediate heterodimer formation with BARD1. BARD1 and BRCA1 are able to form a heterodimer because they both contain ring finger domains that interact with each other. Another main function is to catalyze ubiquination of lysine residue using ubiquitin from E2 enzymes. Ubiquination of lysine-48 is a means of marking a protein for degradation by the proteasome.^[7] BRCA1 also moves to areas within the cell containing damaged DNA and acts as scaffolding for repair complexes to sit.^[8] Ubiquination of lysine-63 controls DNA repair pathways as well as activate protein kinases by sending out non-proteolytic signals.^[9]

Location Summary

RNA sequence shows that BRCA1 is commonly expressed in many tissue types.^[10] Mutations resulting in tumor growth, however, are primarily seen in breast and ovarian tissue. On a subcellular level, BRCA1 is distributed throughout the nucleoplasm in resting and G1 cycling cells. Once the cells prepare to replicate, BRCA1 accumulates into nuclear bodies that also contain BARD1 and other DNA repair proteins. These nuclear bodies act as emergency response teams, ready to be sent to sites of DNA damage.^[11]

Medical Significance

Mutations in BRCA1 are responsible for a large amount of breast and ovarian cancers. Inherited mutations in the RING finger, exons 11-13, and the BRCT domain, along with loss of heterozygosity, are the most common mutations that lead to breast or ovarian cancer.^[12] Specifically, many RING finger E3s play a vital role in maintaining genomic integrity and homeostasis, and as a result are implicated either in the suppression or progression in cancer.^[13] These mutants are also unable to reverse γ-radiation hypersensitivity in addition to becoming incapable of restoring the G2 + M checkpoint in the cell cycle.^[14] A mutation here could result in partial or complete loss of ability of the RING finger to suppress cancerous growths. A frameshift mutation in ovarian epithelial cell lines has also been found to interrupt RING domain function, which ultimately altered caspase 3 activation and lead to staurosporine induced apoptosis.^[15]

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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
3. ↑ Meza, J. E., Brzovic, P. S., King, M., & Kelvin, R. E. (n.d.). Mapping the Functional Domains of BRCA1. Retrieved April 12, 2016, from http://www.jbc.org/content/274/9/5659.full#fn-5 doi: 10.1074/jbc.274.9.5659
4. ↑ Borden, K. L., & Freemont, P. S. (n.d.). The RING finger domain: A recent example of a sequence—structure family. Retrieved April 12, 2016, from http://www.sciencedirect.com/science/article/pii/S0959440X96800601 doi:10.1016/S0959-440X(96)80060-1
5. ↑ Meza, J. E., Brzovic, P. S., King, M., & Kelvin, R. E. (n.d.). Mapping the Functional Domains of BRCA1. Retrieved April 12, 2016, from http://www.jbc.org/content/274/9/5659.full#fn-5 doi: 10.1074/jbc.274.9.5659
6. ↑ Berndsen, C. E.; Wolberger, C. New Insights into Ubiquitin E3 Ligase Mechanism. Nat Struct Mol Biol Nature Structural & Molecular Biology. 2014, 21, 301–307.
7. ↑ Morris, J. R. (2004). BRCA1 : BARD1 induces the formation of conjugated ubiquitin structures, dependent on K6 of ubiquitin, in cells during DNA replication and repair. Human Molecular Genetics, 13(8), 807-817. doi:10.1093/hmg/ddh095
8. ↑ Clapperton, J. A., Manke, I. A., Lowery, D. M., Ho, T., Haire, L. F., Yaffe, M. B., & Smerdon, S. J. (2004). Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat Struct Mol Biol Nature Structural & Molecular Biology, 11(6), 512-518. doi:10.1038/nsmb775
9. ↑ Morris, J. R. (2004). BRCA1 : BARD1 induces the formation of conjugated ubiquitin structures, dependent on K6 of ubiquitin, in cells during DNA replication and repair. Human Molecular Genetics, 13(8), 807-817. doi:10.1093/hmg/ddh095
10. ↑ GeneCards: Human Gene Database. (n.d.). Retrieved April 12, 2016, from http://www.genecards.org/cgi-bin/carddisp.pl?gene=BRCA1#expression, Used to gather information about the BRCA1
11. ↑ Location of BRCA1 in Human Breast and Ovarian Cancer Cells. (n.d.). Retrieved April 12, 2016, from http://science.sciencemag.org/content/272/5258/123 DOI: 10.1126/science.272.5258.123
12. ↑ Clark, S. L., Rodriguez, A. M., Snyder, R. R., Hankins, G. D., & Boehning, D. (n.d.). Structure-Function of the Tumor Suppressor BRCA1. Retrieved April 12, 2016, from https://www.researchgate.net/publication/228072103_Structure-Function_of_the_Tumor_Suppressor_BRCA1 doi:10.5936/csbj.201204005
13. ↑ Lipkowitz, S., & Weissman, A. M. (2011). RINGs of good and evil: RING finger ubiquitin ligases at the crossroads of tumour suppression and oncogenesis. Nature Reviews Cancer Nat Rev Cancer, 11(9), 629-643. doi:10.1038/nrc3120
14. ↑ Ruffner, H., Joazeiro, C. A., Hemmati, D., Hunter, T., & Verma, I. M. (2001, April 24). Cancer-predisposing mutations within the RING domain of BRCA1: Loss of ubiquitin protein ligase activity and protection from radiation hypersensitivity. Retrieved April 12, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC33176/ doi: 10.1073/pnas.081068398
15. ↑ Johnson, N. C., & Kruk, P. A. (2002, July 2). Cancer Cell International. Retrieved April 12, 2016, from http://cancerci.biomedcentral.com/articles/10.1186/1475-2867-2-7 DOI: 10.1186/1475-2867-2-7