User:Isabella Gieck/Sandbox 1
From Proteopedia
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HRP1 found in Saccharomyces cerevisiae
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This is a default text for your page Isabella Gieck/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.
Function
Disease
Relevance
Overall Structural highlights
HRP1 is made up of two RNA binding domains (RBDs) that contain residues serving to facilitate RNA recognition. These two domains fold into a βαββαβ secondary structure in an RNA-free environment, allowing Hrp1 to behave rigidly (source). The includes residues extending from Ser158 to Ala233 and the from Lys244 to Ala318. Both RBDs are composed of a four-stranded beta-sheet with two alpha helices spanning across one side of the sheet. The linker region is made up of Ile234 to Gly243. When RNA is introduced into the environment, conformational change is demonstrated within the linker region and a forms from Arg236 to Lys241. The helix that forms is made up of many charged polar residues that stabilize themselves through between Arg236-Asp240 and Asp237-Lys241.
Hrp1 identifies the polyadenylation enhancement element (PEE) in the 3' UTR of RNA through Van Der Waals interactions and Hydrogen bonding. The PEE is made up of UAUAUA sequence in which HRP1 recognizes and binds. The association of these RBD domains aids in binding through the development of a deep highly positively charged cleft between the two. This cleft is v-shaped, accommodating the RNA very well. Some RNA bases have been revealed to be buried within protein pockets while some are observed in between protein loops. The recognition of RNA by Hrp1 is entirely dominated by RNA-protein interactions. The absence of RNA base pairing or RNA base-base stacking which have been observed in similar complexes (***) might explain the ability of Hrp1 to target short RNA sequences in comparison to those recognized by similar proteins.
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References
- ↑ 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
