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5egs

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Revision as of 06:57, 22 April 2020

Human PRMT6 with bound fragment-type inhibitor

Structural highlights

5egs is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	4qpp
Gene:	PRMT6, HRMT1L6 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ANM6_HUMAN] Arginine methyltransferase that can catalyze the formation of both omega-N monomethylarginine (MMA) and asymmetrical dimethylarginine (aDMA), with a strong preference for the formation of aDMA. Preferentially methylates arginyl residues present in a glycine and arginine-rich domain and displays preference for monomethylated substrates. Specifically mediates the asymmetric dimethylation of histone H3 'Arg-2' to form H3R2me2a. H3R2me2a represents a specific tag for epigenetic transcriptional repression and is mutually exclusive with methylation on histone H3 'Lys-4' (H3K4me2 and H3K4me3). Acts as a transcriptional repressor of various genes such as HOXA2, THBS1 and TP53. Repression of TP53 blocks cellular senescence (By similarity). Also methylates histone H2A and H4 'Arg-3' (H2AR3me and H4R3me, respectively). Acts as a regulator of DNA base excision during DNA repair by mediating the methylation of DNA polymerase beta (POLB), leading to the stimulation of its polymerase activity by enhancing DNA binding and processivity. Methylates HMGA1. Regulates alternative splicing events. Acts as a transcriptional coactivator of a number of steroid hormone receptors including ESR1, ESR2, PGR and NR3C1. Promotes fasting-induced transcriptional activation of the gluconeogenic program through methylation of the CRTC2 transcription coactivator. May play a role in innate immunity against HIV-1 in case of infection by methylating and impairing the function of various HIV-1 proteins such as Tat, Rev and Nucleocapsid protein p7 (NC).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Publication Abstract from PubMed

Protein methyltransferases (PMTs) are a promising target class in oncology and other disease areas. They are composed of SET domain methyltransferases and structurally unrelated Rossman-fold enzymes that include protein arginine methyltransferases (PRMTs). In the absence of a well-defined medicinal chemistry tool-kit focused on PMTs, most current inhibitors were identified by screening large and diverse libraries of leadlike molecules. So far, no successful fragment-based approach was reported against this target class. Here, by deconstructing potent PRMT inhibitors, we find that chemical moieties occupying the substrate arginine-binding site can act as efficient fragment inhibitors. Screening a fragment library against PRMT6 produced numerous hits, including a 300 nM inhibitor (ligand efficiency of 0.56) that decreased global histone 3 arginine 2 methylation in cells, and can serve as a warhead for the development of PRMT chemical probes.

Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.,Ferreira de Freitas R, Eram MS, Szewczyk MM, Steuber H, Smil D, Wu H, Li F, Senisterra G, Dong A, Brown PJ, Hitchcock M, Moosmayer D, Stegmann CM, Egner U, Arrowsmith C, Barsyte-Lovejoy D, Vedadi M, Schapira M J Med Chem. 2016 Feb 11;59(3):1176-83. doi: 10.1021/acs.jmedchem.5b01772. Epub, 2016 Jan 29. PMID:26824386^[12]

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

References

↑ Frankel A, Yadav N, Lee J, Branscombe TL, Clarke S, Bedford MT. The novel human protein arginine N-methyltransferase PRMT6 is a nuclear enzyme displaying unique substrate specificity. J Biol Chem. 2002 Feb 1;277(5):3537-43. Epub 2001 Nov 27. PMID:11724789 doi:http://dx.doi.org/10.1074/jbc.M108786200
↑ Miranda TB, Webb KJ, Edberg DD, Reeves R, Clarke S. Protein arginine methyltransferase 6 specifically methylates the nonhistone chromatin protein HMGA1a. Biochem Biophys Res Commun. 2005 Oct 28;336(3):831-5. PMID:16157300 doi:http://dx.doi.org/10.1016/j.bbrc.2005.08.179
↑ Herrmann F, Lee J, Bedford MT, Fackelmayer FO. Dynamics of human protein arginine methyltransferase 1(PRMT1) in vivo. J Biol Chem. 2005 Nov 11;280(45):38005-10. Epub 2005 Sep 13. PMID:16159886 doi:http://dx.doi.org/10.1074/jbc.M502458200
↑ El-Andaloussi N, Valovka T, Toueille M, Steinacher R, Focke F, Gehrig P, Covic M, Hassa PO, Schar P, Hubscher U, Hottiger MO. Arginine methylation regulates DNA polymerase beta. Mol Cell. 2006 Apr 7;22(1):51-62. PMID:16600869 doi:http://dx.doi.org/10.1016/j.molcel.2006.02.013
↑ Xie B, Invernizzi CF, Richard S, Wainberg MA. Arginine methylation of the human immunodeficiency virus type 1 Tat protein by PRMT6 negatively affects Tat Interactions with both cyclin T1 and the Tat transactivation region. J Virol. 2007 Apr;81(8):4226-34. Epub 2007 Jan 31. PMID:17267505 doi:http://dx.doi.org/10.1128/JVI.01888-06
↑ Guccione E, Bassi C, Casadio F, Martinato F, Cesaroni M, Schuchlautz H, Luscher B, Amati B. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature. 2007 Oct 18;449(7164):933-7. Epub 2007 Sep 26. PMID:17898714 doi:http://dx.doi.org/10.1038/nature06166
↑ Hyllus D, Stein C, Schnabel K, Schiltz E, Imhof A, Dou Y, Hsieh J, Bauer UM. PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev. 2007 Dec 15;21(24):3369-80. PMID:18079182 doi:http://dx.doi.org/10.1101/gad.447007
↑ Iberg AN, Espejo A, Cheng D, Kim D, Michaud-Levesque J, Richard S, Bedford MT. Arginine methylation of the histone H3 tail impedes effector binding. J Biol Chem. 2008 Feb 8;283(6):3006-10. Epub 2007 Dec 11. PMID:18077460 doi:http://dx.doi.org/10.1074/jbc.C700192200
↑ Lakowski TM, Frankel A. Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4. Biochem J. 2009 Jun 26;421(2):253-61. doi: 10.1042/BJ20090268. PMID:19405910 doi:10.1042/BJ20090268
↑ Michaud-Levesque J, Richard S. Thrombospondin-1 is a transcriptional repression target of PRMT6. J Biol Chem. 2009 Aug 7;284(32):21338-46. doi: 10.1074/jbc.M109.005322. Epub 2009, Jun 9. PMID:19509293 doi:http://dx.doi.org/10.1074/jbc.M109.005322
↑ Harrison MJ, Tang YH, Dowhan DH. Protein arginine methyltransferase 6 regulates multiple aspects of gene expression. Nucleic Acids Res. 2010 Apr;38(7):2201-16. doi: 10.1093/nar/gkp1203. Epub 2010, Jan 4. PMID:20047962 doi:http://dx.doi.org/10.1093/nar/gkp1203
↑ Ferreira de Freitas R, Eram MS, Szewczyk MM, Steuber H, Smil D, Wu H, Li F, Senisterra G, Dong A, Brown PJ, Hitchcock M, Moosmayer D, Stegmann CM, Egner U, Arrowsmith C, Barsyte-Lovejoy D, Vedadi M, Schapira M. Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor. J Med Chem. 2016 Feb 11;59(3):1176-83. doi: 10.1021/acs.jmedchem.5b01772. Epub, 2016 Jan 29. PMID:26824386 doi:http://dx.doi.org/10.1021/acs.jmedchem.5b01772

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5egs"

@@ Line 1: / Line 1: @@
 ==Human PRMT6 with bound fragment-type inhibitor==
-<StructureSection load='5egs' size='340' side='right' caption='[[5egs]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='5egs' size='340' side='right'caption='[[5egs]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5egs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EGS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5egs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EGS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EGS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5NR:2-[4-(PHENYLMETHYL)PIPERIDIN-1-YL]ETHANAMINE'>5NR</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5NR:2-[4-(PHENYLMETHYL)PIPERIDIN-1-YL]ETHANAMINE'>5NR</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qpp|4qpp]]</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=5egs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egs OCA], [http://pdbe.org/5egs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5egs RCSB], [http://www.ebi.ac.uk/pdbsum/5egs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5egs ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRMT6, HRMT1L6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5egs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5egs OCA], [http://pdbe.org/5egs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5egs RCSB], [http://www.ebi.ac.uk/pdbsum/5egs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5egs ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5egs" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Brown, P J]]
 [[Category: Egner, U]]

5egs

From Proteopedia

Revision as of 06:57, 22 April 2020

Human PRMT6 with bound fragment-type inhibitor

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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