4rcm: Difference between revisions

Latest revision as of 13:23, 1 July 2026

Crystal structure of the Pho92 YTH domain in complex with m6A

Structural highlights

4rcm is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	6MZ
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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:https://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:https://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:https://dx.doi.org/10.1074/jbc.M115.680389

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1042/BJ20130862

[2] 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:https://dx.doi.org/10.1016/j.cell.2013.10.047

[3] 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:https://dx.doi.org/10.1074/jbc.M115.680389

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@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[4rcm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RCM FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4rcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rcm OCA], [https://pdbe.org/4rcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rcm RCSB], [https://www.ebi.ac.uk/pdbsum/4rcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rcm ProSAT]</span></td></tr>
 </table>

4rcm: Difference between revisions

Latest revision as of 13:23, 1 July 2026

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?)

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