This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4rcm

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 23:40, 21 October 2015

Crystal structure of the Pho92 YTH domain in complex with m6A

Structural highlights

4rcm is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	4rci, 4rcj
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[MRB1_YEAST] RNA-binding protein that acts as a post-transcriptional regulator of phosphate metabolism by binding to the 3'-UTR region of PHO4 mRNA, decreasing its stability. Acts by recognizing and binding N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs.^[1] ^[2]

Publication Abstract from PubMed

N6-methyladenosine (m6A) is the most abundant internal modification in RNA and is specifically recognized by YTH domain containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m6A nucleotide in RNA and preferentially binds to the GG(m6A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92, and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m6A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m6A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m6A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbours a distinctly selective binding pocket for the nucleotide preceding the m6A nucleotide.

Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins.,Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J J Biol Chem. 2015 Aug 28. pii: jbc.M115.680389. PMID:26318451^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kang HJ, Jeong SJ, Kim KN, Baek IJ, Chang M, Kang CM, Park YS, Yun CW. A novel protein, Pho92, has a conserved YTH domain and regulates phosphate metabolism by decreasing the mRNA stability of PHO4 in Saccharomyces cerevisiae. Biochem J. 2014 Feb 1;457(3):391-400. doi: 10.1042/BJ20130862. PMID:24206186 doi:http://dx.doi.org/10.1042/BJ20130862
↑ Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013 Dec 5;155(6):1409-21. doi: 10.1016/j.cell.2013.10.047. Epub 2013 Nov, 21. PMID:24269006 doi:http://dx.doi.org/10.1016/j.cell.2013.10.047
↑ Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J. Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins. J Biol Chem. 2015 Aug 28. pii: jbc.M115.680389. PMID:26318451 doi:http://dx.doi.org/10.1074/jbc.M115.680389

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rcm"

@@ Line 6: / Line 6: @@
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rci|4rci]], [[4rcj|4rcj]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rcm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rcm RCSB], [http://www.ebi.ac.uk/pdbsum/4rcm PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rcm OCA], [http://pdbe.org/4rcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rcm RCSB], [http://www.ebi.ac.uk/pdbsum/4rcm PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4rcm" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4rcm

From Proteopedia

Revision as of 23:40, 21 October 2015

Crystal structure of the Pho92 YTH domain in complex with m6A

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox